![]() | This ![]() It is of interest to the following WikiProjects: | ||||||||||||||||
|
"Evolutionary kibble"? I think you mean evolutionary "kipple", as per Philip K. Dick. 204.209.121.10 18:55, 5 March 2007 (UTC)
This is cited as a piece of evidence in support of evolution. By whom?
know if you ever care to read one. --LDC
Cf. dead code in most larger software systems...
Where he copied it from is of no improtance. This is established truth. The textbook Biology by Neil A. Campbell and Jane B. Reece states that introns may be spliced out in differnent ways to combine different exons from one gene. This mRNA will code for different proteins with new and possibly novel functions. These new proteins may allow one organism to survive better than another organism of the same species. It will live on to pass on its genetic information while others will not. If that is not evolution than I don't know what is.-- Swimmer678 04:11, 15 November 2006 (UTC)
"Junk DNA" is not a well-defined term, of course, but I would hesitate to say that it is synonymous with intron DNA. A lot of noncoding DNA that is never transcribed into RNA in the first place exists, and I believe that it is usually also considered to be "junk" DNA when factoids about how 90% or whatever of human DNA is junk are bandied about. Bryan Derksen
The diagram a the top is neither informative nor accurate – wouldn't the one beneath it be just as good?
Group I and group II introns are mentioned. What about pre-mRNA introns? They are the ones that your figure shows. What about mentioning how introns are spliced out?
Also, there are plenty of references showing that introns are not "junk DNA", on the contrary some contain regulatory elements necessary for expression. I think this should be made clear.
"Introns are sections of DNA that will be spliced out after transcription" – sounds ambiguous, as if the pieces of DNA will be spliced out. RNA is mentioned later but in my opinion somebody not familiar with terminology might be confused Vicki Doronina 18:01, 13 January 2007 (UTC)
Just curious, but could we change the first sentence to something like "introns are transcribed but non translated regions of dna" and contrast them to exons? Seems like it would be less ambiguous than the current wording.
The Intron article says that in prokaryotes, introns only occur in tRNA and rRNA. The group II intron article, however, says they occur in mRNA. I realize that this is not necessarily a contradiction, but could someone please clarify it? -- aciel ( talk) 18:40, 27 November 2007 (UTC)
The article has a paragraph about how "higher" organisms (whatever that means) have many introns, while some "less advanced" (?) organisms have few introns. Does anyone have any data to suggest that mammals have more introns than other ophistokonts, and that the average land plant has more introns than protists like algae or dinoflagellates? Of course there is a vague connection between organism size and total genome size, but I don't think there is a connection for intron number or density. Ostreoccoccus for example, despite being perhaps the smallest eukaryote, with a relatively compact genome, has a very high intron density. The smallest known eukaryotic genome (nucleomorph) of chloroachnion has an average intron density despite its tininess. Whether or not one subscribes to an introns early or late hypothesis, it is clear that there is an extremely diverse pattern of intron distribution and density that defies a simple explanation of higher organsisms = many introns, lower organisms = few introns Spamburgler ( talk) 10:23, 7 August 2008 (UTC)
"Genes of higher organisms, such as mammals and flowering plants, have numerous introns, which can be much longer than the nearby exons. Some less advanced organisms, such as fungus Saccharomyces cerevisiae, and protists, have very few introns." This is wrong on many levels.
Narayanese ( talk) 05:22, 11 August 2008 (UTC)
I guess part of the problem here is the use of the non-scientific concept of "higher" and "lower". These are old fashioned terms that may indeed be familiar to 15 year olds, but in fact do not impart meaningful scientific information, other than an erroneous impression of directed evolution, or a religous based view of biology with humans "higher" on the scale. "Higher" is sometimes used to convey multicellularity, or even in some cases size of organism, or in others size of genome. The terms might also imply number of genes – although presumably not in the last 10 years. Alternatively, the term could be used to mean organisms belonging to phyla with slowly evolving gene sequences. In a scientific context the term was sometimes applied to "crown eukaroytes" a grouping that is now generally recognised as not reflecting any genuine phyletic relationship. Clearly, many of these meanings are mutually inconsistent, and we cannot apply the terms here without unecessary ambiguity. The references to yeast/funghi /land plants/green algae/animals highlight the danger of using such ambiguous language. Clearly yeast is closely related to multicellular funghi and animals, and more distantly related to angiosperms, gymnosperms, green algae and other Plantae. The observation (not sure if it is true) that multicellular funghi generally have more introns than S. cerevisiae, and that angiosperms have more than most funghi demonstrates, while some other plantae have much few introns, demonstrates that intron density can be greatly variable within phylogenetic groups. It may follow some interesting trends, but the reduction of this trend to a nonsensical "higher and lower" does it no justice.
Several points of interest are worthy of discussion, and which are unclear in my mind;
1. That some deep branching phyla (eg excavata?) have few introns (may be true, but certainly lots of exceptions, and lots of reversions within recent branching groups)
2. That multicellular organisms have more introns per gene than unicellular organisms (may be true – though probably not enough sampling to know yet).
Does anyone have any knowledge of these specific questions? Spamburgler ( talk) 07:09, 13 August 2008 (UTC)
Wow guys, this is really quite sad. Not only are you in an arguement over semantics, but you're dragging it out to the point where this one segment is taking up about a fourth of the talk page. While it's true that a lot of these are generalizations with exceptions that seem to make them irrefutably untrue, every rule has it's exceptions. One or two examples that go against a generalized trend are not enough to break the trend down. That being said, you guys need to get over yourselves here. if you want to talk genetics, how about this: 75% of our genes are shared with worms, 98% with chimps, and about half with bananas. Why don't you contemplate why, with all those similarities, humans are the only species as of yet capable of fighting over wether someone is right, or right in a slightly different way. have fun with that, my argue-mental friends. —Preceding unsigned comment added by 71.227.217.60 ( talk) 22:05, 8 December 2009 (UTC)
Hi wikipedians, what is the key difference between introns and noncoding DNA... merge? -- Vojtech.dostal ( talk) 07:32, 25 August 2008 (UTC)
I don't think this is elsewhere discussed on this page, but there's a small but imprtant inaccuracy in the definition of an intron, where it states: "(Introns are) DNA regions in a gene that are not translated into proteins." While this is true, I'm not sure it's very accurate, and I suggest that it be modified to something like "(introns are) DNA regions which are removed by the joining of the two flanking exonic sequences, and thus are not represented in the mature RNA product" A bit clumsy i know, but I've got to have dinner... Thoughts? if there are no objections, I'll re-write the above and put it in... Geno-Supremo ( talk) 20:11, 11 November 2008 (UTC)
Hello fellow Wikipedians,
Getting back at the above discussion: I really do think the first bit of the article should be changed. An intron doesn't code for the protein that the surrounding exons code for BUT it might code for a maturase (a protein needed for splicing). I can add citation but it is also mentioned in the article under 'Classification'. I will think about a decent sentencence (I am not a native English speaker) and post it here for you to comment on. WKoets ( talk) 16:00, 21 September 2009 (UTC)
References
Introns may also contain "old code", or sections of a gene that were once translated into a protein, but have since become inactive. It was generally assumed that the sequence of any given intron is Junk DNA with no biological function. More recently, however, this is being disputed.
I don't think this is strong enough. That at least some introns are functional and adaptive as opposed to relics is now the mainstream view amongst geneticists.
For proof, a few recent journals:
{{
cite journal}}
: CS1 maint: unflagged free DOI (
link)
Besides, the journal cited for the more recently ... this is being disputed was published almost 15 years ago.
Jebus989
★
15:25, 25 April 2010 (UTC)
About Intron#Simple_illustration_of_an_intron_and_RNA_splicing: This seems a little too "instructional textbook" rather than "encyclopedia article" to me. What do other people think? WhatamIdoing ( talk) 19:55, 7 March 2011 (UTC)
Shouldn't it be moved to RNA_splicing? Klortho ( talk) 14:06, 24 February 2012 (UTC)
It's good to have an illustration here but this one is inaccurate. A UTR is part of an exon. Compare this illustration with the one in the Exon article ( /info/en/?search=File:Gene_structure.svg) Mutundis ( talk) 23:34, 1 September 2015 (UTC)
This is my attempt at a better illustration IMHO:
— Preceding unsigned comment added by Mutundis ( talk • contribs) 01:19, 2 September 2015 (UTC)
Is it worth mentioning that some authors (such as Greg Bear) have fictionally hypothesised that introns are used to store memories in cells? — Preceding unsigned comment added by 92.24.51.92 ( talk) 12:13, 27 August 2013 (UTC)
What is the reasoning behind the following statement?: "Since eukaryotes arose from a common ancestor (Common descent), there must have been extensive gain or loss of introns during evolutionary time.[23][24] This process is thought to be subject to selection, with a tendency towards intron gain in larger species due to their smaller population sizes, and the converse in smaller (particularly unicellular) species.[25]" ZFT ( talk) 19:29, 26 February 2015 (UTC)
Introns are well known in bacterial and archaeal genes, but occur more rarely than in most eukaryotic genomes.[citation needed] A particularly extreme case is the Drosophila dhc7 gene containing a ≥3.6 Mb intron, which takes roughly three days to transcribe.[9][10]
This is ambiguous. The reference to cases found "more rarely" is then followed by what appears to be an example of "a particularly extreme case", but this turns out to be an example, not of the rarely found cases, but of a genome with particularly abundant introns referred to earlier. Myles325a ( talk) 05:27, 7 December 2015 (UTC)
Introns are well known in bacterial and archaeal genes, but occur more rarely than in most eukaryotic genomes.[citation needed] A particularly extreme case is the Drosophila dhc7 gene containing a ≥3.6 Mb intron, which takes roughly three days to transcribe.[9][10]
This is ambiguous. The reference to cases found "more rarely" is then followed by what appears to be an example of "a particularly extreme case", but this turns out to be an example, not of the rarely found cases, but of a genome with particularly abundant introns referred to earlier. Myles325a ( talk) 05:27, 7 December 2015 (UTC)
The comment(s) below were originally left at Talk:Intron/Comments, and are posted here for posterity. Following several discussions in past years, these subpages are now deprecated. The comments may be irrelevant or outdated; if so, please feel free to remove this section.
Rated "high" as high school/SAT biology content, part of gene structure. - tameeria 23:56, 18 February 2007 (UTC) |
Last edited at 23:56, 18 February 2007 (UTC). Substituted at 19:02, 29 April 2016 (UTC)
The article contains references to 14 and 15 year old textbooks. Are references to textbooks really necessary? A good Wikipedia article should be at least as authoritative as a textbook. (I say this as a textbook author.) I suggest replacing textbook references with references to recent reviews in primary literature. Genome42 ( talk) 15:00, 19 May 2022 (UTC)
The introduction is confusing because the first part only refers to introns in protein-coding genes. It also contains references to 14 and 15 year old textbooks and other references that are inappropriate.
I propose editing the introduction to make it more accurate and more relevant. Genome42 ( talk) 15:03, 19 May 2022 (UTC)
A good case can be made that introns are mostly junk DNA but that case isn't made in the article. That needs to be fixed.
I have proposed creating a separate Wikipedia entry on Junk DNA and I am actively working on it. The proposal is being discussed in the Talk section on the Noncoding DNA page. Please add your views on this proposal, which I think is long overdue. Genome42 ( talk) 15:35, 19 May 2022 (UTC)
I'm working on a new section with the tentative title "On the accuracy of splicing." The goal is to present the evidence showing that splicing is quite error-prone and that cells are expected to contain large numbers of incorrectly spliced transcripts due to mistakes in splicing. This is important because these splicing artifacts are easily detected by modern techniques and their sequences are entered into the transcript databases. Most of them are recognized and ignored by genome annotators but a significant number have made it into the standard reference genome. This leads to considerable confusion about alternative splicing because it is often assumed, without evidence, that these transcripts are biologically relevant leading to rather extraordinary claims about the prevalence of alternative splicing. Those false (IMHO) claims are prominently mentioned in this article but the counter-arguments also have to be addressed in order to provide balance.
Here's a blog post that I published two years ago. It discusses the problem and the pervasive bias in the scientific literature.
https://sandwalk.blogspot.com/2020/04/alternative-splicing-function-vs-noise.html
Genome42 ( talk) 14:09, 21 May 2022 (UTC)
![]() | This ![]() It is of interest to the following WikiProjects: | ||||||||||||||||
|
"Evolutionary kibble"? I think you mean evolutionary "kipple", as per Philip K. Dick. 204.209.121.10 18:55, 5 March 2007 (UTC)
This is cited as a piece of evidence in support of evolution. By whom?
know if you ever care to read one. --LDC
Cf. dead code in most larger software systems...
Where he copied it from is of no improtance. This is established truth. The textbook Biology by Neil A. Campbell and Jane B. Reece states that introns may be spliced out in differnent ways to combine different exons from one gene. This mRNA will code for different proteins with new and possibly novel functions. These new proteins may allow one organism to survive better than another organism of the same species. It will live on to pass on its genetic information while others will not. If that is not evolution than I don't know what is.-- Swimmer678 04:11, 15 November 2006 (UTC)
"Junk DNA" is not a well-defined term, of course, but I would hesitate to say that it is synonymous with intron DNA. A lot of noncoding DNA that is never transcribed into RNA in the first place exists, and I believe that it is usually also considered to be "junk" DNA when factoids about how 90% or whatever of human DNA is junk are bandied about. Bryan Derksen
The diagram a the top is neither informative nor accurate – wouldn't the one beneath it be just as good?
Group I and group II introns are mentioned. What about pre-mRNA introns? They are the ones that your figure shows. What about mentioning how introns are spliced out?
Also, there are plenty of references showing that introns are not "junk DNA", on the contrary some contain regulatory elements necessary for expression. I think this should be made clear.
"Introns are sections of DNA that will be spliced out after transcription" – sounds ambiguous, as if the pieces of DNA will be spliced out. RNA is mentioned later but in my opinion somebody not familiar with terminology might be confused Vicki Doronina 18:01, 13 January 2007 (UTC)
Just curious, but could we change the first sentence to something like "introns are transcribed but non translated regions of dna" and contrast them to exons? Seems like it would be less ambiguous than the current wording.
The Intron article says that in prokaryotes, introns only occur in tRNA and rRNA. The group II intron article, however, says they occur in mRNA. I realize that this is not necessarily a contradiction, but could someone please clarify it? -- aciel ( talk) 18:40, 27 November 2007 (UTC)
The article has a paragraph about how "higher" organisms (whatever that means) have many introns, while some "less advanced" (?) organisms have few introns. Does anyone have any data to suggest that mammals have more introns than other ophistokonts, and that the average land plant has more introns than protists like algae or dinoflagellates? Of course there is a vague connection between organism size and total genome size, but I don't think there is a connection for intron number or density. Ostreoccoccus for example, despite being perhaps the smallest eukaryote, with a relatively compact genome, has a very high intron density. The smallest known eukaryotic genome (nucleomorph) of chloroachnion has an average intron density despite its tininess. Whether or not one subscribes to an introns early or late hypothesis, it is clear that there is an extremely diverse pattern of intron distribution and density that defies a simple explanation of higher organsisms = many introns, lower organisms = few introns Spamburgler ( talk) 10:23, 7 August 2008 (UTC)
"Genes of higher organisms, such as mammals and flowering plants, have numerous introns, which can be much longer than the nearby exons. Some less advanced organisms, such as fungus Saccharomyces cerevisiae, and protists, have very few introns." This is wrong on many levels.
Narayanese ( talk) 05:22, 11 August 2008 (UTC)
I guess part of the problem here is the use of the non-scientific concept of "higher" and "lower". These are old fashioned terms that may indeed be familiar to 15 year olds, but in fact do not impart meaningful scientific information, other than an erroneous impression of directed evolution, or a religous based view of biology with humans "higher" on the scale. "Higher" is sometimes used to convey multicellularity, or even in some cases size of organism, or in others size of genome. The terms might also imply number of genes – although presumably not in the last 10 years. Alternatively, the term could be used to mean organisms belonging to phyla with slowly evolving gene sequences. In a scientific context the term was sometimes applied to "crown eukaroytes" a grouping that is now generally recognised as not reflecting any genuine phyletic relationship. Clearly, many of these meanings are mutually inconsistent, and we cannot apply the terms here without unecessary ambiguity. The references to yeast/funghi /land plants/green algae/animals highlight the danger of using such ambiguous language. Clearly yeast is closely related to multicellular funghi and animals, and more distantly related to angiosperms, gymnosperms, green algae and other Plantae. The observation (not sure if it is true) that multicellular funghi generally have more introns than S. cerevisiae, and that angiosperms have more than most funghi demonstrates, while some other plantae have much few introns, demonstrates that intron density can be greatly variable within phylogenetic groups. It may follow some interesting trends, but the reduction of this trend to a nonsensical "higher and lower" does it no justice.
Several points of interest are worthy of discussion, and which are unclear in my mind;
1. That some deep branching phyla (eg excavata?) have few introns (may be true, but certainly lots of exceptions, and lots of reversions within recent branching groups)
2. That multicellular organisms have more introns per gene than unicellular organisms (may be true – though probably not enough sampling to know yet).
Does anyone have any knowledge of these specific questions? Spamburgler ( talk) 07:09, 13 August 2008 (UTC)
Wow guys, this is really quite sad. Not only are you in an arguement over semantics, but you're dragging it out to the point where this one segment is taking up about a fourth of the talk page. While it's true that a lot of these are generalizations with exceptions that seem to make them irrefutably untrue, every rule has it's exceptions. One or two examples that go against a generalized trend are not enough to break the trend down. That being said, you guys need to get over yourselves here. if you want to talk genetics, how about this: 75% of our genes are shared with worms, 98% with chimps, and about half with bananas. Why don't you contemplate why, with all those similarities, humans are the only species as of yet capable of fighting over wether someone is right, or right in a slightly different way. have fun with that, my argue-mental friends. —Preceding unsigned comment added by 71.227.217.60 ( talk) 22:05, 8 December 2009 (UTC)
Hi wikipedians, what is the key difference between introns and noncoding DNA... merge? -- Vojtech.dostal ( talk) 07:32, 25 August 2008 (UTC)
I don't think this is elsewhere discussed on this page, but there's a small but imprtant inaccuracy in the definition of an intron, where it states: "(Introns are) DNA regions in a gene that are not translated into proteins." While this is true, I'm not sure it's very accurate, and I suggest that it be modified to something like "(introns are) DNA regions which are removed by the joining of the two flanking exonic sequences, and thus are not represented in the mature RNA product" A bit clumsy i know, but I've got to have dinner... Thoughts? if there are no objections, I'll re-write the above and put it in... Geno-Supremo ( talk) 20:11, 11 November 2008 (UTC)
Hello fellow Wikipedians,
Getting back at the above discussion: I really do think the first bit of the article should be changed. An intron doesn't code for the protein that the surrounding exons code for BUT it might code for a maturase (a protein needed for splicing). I can add citation but it is also mentioned in the article under 'Classification'. I will think about a decent sentencence (I am not a native English speaker) and post it here for you to comment on. WKoets ( talk) 16:00, 21 September 2009 (UTC)
References
Introns may also contain "old code", or sections of a gene that were once translated into a protein, but have since become inactive. It was generally assumed that the sequence of any given intron is Junk DNA with no biological function. More recently, however, this is being disputed.
I don't think this is strong enough. That at least some introns are functional and adaptive as opposed to relics is now the mainstream view amongst geneticists.
For proof, a few recent journals:
{{
cite journal}}
: CS1 maint: unflagged free DOI (
link)
Besides, the journal cited for the more recently ... this is being disputed was published almost 15 years ago.
Jebus989
★
15:25, 25 April 2010 (UTC)
About Intron#Simple_illustration_of_an_intron_and_RNA_splicing: This seems a little too "instructional textbook" rather than "encyclopedia article" to me. What do other people think? WhatamIdoing ( talk) 19:55, 7 March 2011 (UTC)
Shouldn't it be moved to RNA_splicing? Klortho ( talk) 14:06, 24 February 2012 (UTC)
It's good to have an illustration here but this one is inaccurate. A UTR is part of an exon. Compare this illustration with the one in the Exon article ( /info/en/?search=File:Gene_structure.svg) Mutundis ( talk) 23:34, 1 September 2015 (UTC)
This is my attempt at a better illustration IMHO:
— Preceding unsigned comment added by Mutundis ( talk • contribs) 01:19, 2 September 2015 (UTC)
Is it worth mentioning that some authors (such as Greg Bear) have fictionally hypothesised that introns are used to store memories in cells? — Preceding unsigned comment added by 92.24.51.92 ( talk) 12:13, 27 August 2013 (UTC)
What is the reasoning behind the following statement?: "Since eukaryotes arose from a common ancestor (Common descent), there must have been extensive gain or loss of introns during evolutionary time.[23][24] This process is thought to be subject to selection, with a tendency towards intron gain in larger species due to their smaller population sizes, and the converse in smaller (particularly unicellular) species.[25]" ZFT ( talk) 19:29, 26 February 2015 (UTC)
Introns are well known in bacterial and archaeal genes, but occur more rarely than in most eukaryotic genomes.[citation needed] A particularly extreme case is the Drosophila dhc7 gene containing a ≥3.6 Mb intron, which takes roughly three days to transcribe.[9][10]
This is ambiguous. The reference to cases found "more rarely" is then followed by what appears to be an example of "a particularly extreme case", but this turns out to be an example, not of the rarely found cases, but of a genome with particularly abundant introns referred to earlier. Myles325a ( talk) 05:27, 7 December 2015 (UTC)
Introns are well known in bacterial and archaeal genes, but occur more rarely than in most eukaryotic genomes.[citation needed] A particularly extreme case is the Drosophila dhc7 gene containing a ≥3.6 Mb intron, which takes roughly three days to transcribe.[9][10]
This is ambiguous. The reference to cases found "more rarely" is then followed by what appears to be an example of "a particularly extreme case", but this turns out to be an example, not of the rarely found cases, but of a genome with particularly abundant introns referred to earlier. Myles325a ( talk) 05:27, 7 December 2015 (UTC)
The comment(s) below were originally left at Talk:Intron/Comments, and are posted here for posterity. Following several discussions in past years, these subpages are now deprecated. The comments may be irrelevant or outdated; if so, please feel free to remove this section.
Rated "high" as high school/SAT biology content, part of gene structure. - tameeria 23:56, 18 February 2007 (UTC) |
Last edited at 23:56, 18 February 2007 (UTC). Substituted at 19:02, 29 April 2016 (UTC)
The article contains references to 14 and 15 year old textbooks. Are references to textbooks really necessary? A good Wikipedia article should be at least as authoritative as a textbook. (I say this as a textbook author.) I suggest replacing textbook references with references to recent reviews in primary literature. Genome42 ( talk) 15:00, 19 May 2022 (UTC)
The introduction is confusing because the first part only refers to introns in protein-coding genes. It also contains references to 14 and 15 year old textbooks and other references that are inappropriate.
I propose editing the introduction to make it more accurate and more relevant. Genome42 ( talk) 15:03, 19 May 2022 (UTC)
A good case can be made that introns are mostly junk DNA but that case isn't made in the article. That needs to be fixed.
I have proposed creating a separate Wikipedia entry on Junk DNA and I am actively working on it. The proposal is being discussed in the Talk section on the Noncoding DNA page. Please add your views on this proposal, which I think is long overdue. Genome42 ( talk) 15:35, 19 May 2022 (UTC)
I'm working on a new section with the tentative title "On the accuracy of splicing." The goal is to present the evidence showing that splicing is quite error-prone and that cells are expected to contain large numbers of incorrectly spliced transcripts due to mistakes in splicing. This is important because these splicing artifacts are easily detected by modern techniques and their sequences are entered into the transcript databases. Most of them are recognized and ignored by genome annotators but a significant number have made it into the standard reference genome. This leads to considerable confusion about alternative splicing because it is often assumed, without evidence, that these transcripts are biologically relevant leading to rather extraordinary claims about the prevalence of alternative splicing. Those false (IMHO) claims are prominently mentioned in this article but the counter-arguments also have to be addressed in order to provide balance.
Here's a blog post that I published two years ago. It discusses the problem and the pervasive bias in the scientific literature.
https://sandwalk.blogspot.com/2020/04/alternative-splicing-function-vs-noise.html
Genome42 ( talk) 14:09, 21 May 2022 (UTC)