Talk:Mutation

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Wiki Education Foundation-supported course assignment
This article was the subject of a Wiki Education Foundation-supported course assignment, between 28 August 2018 and 21 December 2018. Further details are available on the course page. Student editor(s): Damonie667.

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Wiki Education Foundation-supported course assignment
This article is or was the subject of a Wiki Education Foundation-supported course assignment. Further details are available on the course page. Student editor(s): Dishabhavsar. Peer reviewers: Ddoerflinger, HadeelBinomar.

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Citation needed for "mutations are generally harmful" ?
Under "Beneficial mutations": "Although most mutations that change protein sequences are neutral or harmful[citation needed], some... " Can we remove [citation needed]? How often do you see undesired changes to a complex code result in a positive change? It's common knowledge that mutations cause countless diseases and syndromes. Positive or even neutral mutations are negligible compared to the damage they cause. Precise wording: "Although mutations that change protein sequences are predominantly harmful; on occasion, they can have neutral or positive effects." — Preceding unsigned comment added by 64.198.192.11 (talk) 17:00, 31 August 2011 (UTC)
 * Well, citation is necessary because it is an assertion. You only read about the mutations that causes disease because they are worth studying, most mutations probably don't make any significant difference. Hzh (talk) 00:05, 2 December 2011 (UTC)

Generally speaking, most mutations are very slightly harmful, in the sense that they lead away from adaptation to current circumstances. A good citation for this would be ISBN 978-0198569732, which uses similar words to say this point. This could be good to include in the arguments about beneficial vs deleterious mutation. — Preceding unsigned comment added by 96.43.225.7 (talk) 23:17, 3 November 2012 (UTC)


 * The problem it seems is that people seem to be concentrating on mutations within genes. There are studies that show that mutations outside of genes are mostly harmless.  Mutation does not mean mutation in genes only or change in protein sequence, and that needs to be made clearer.  Hzh (talk) 22:13, 7 December 2012 (UTC)

DNA_error redirects to Kurzweils "Singularity is Near"
The "error" link redirects to the "Singularity is Near" book by Ray Kurzweil. That can't possibly be correct. Qed (talk) 14:13, 2 January 2012 (UTC)
 * This refers to the DNA error link in "as well as errors that occur during meiosis or DNA replication" in the lead. Since 5 November 2011, that page is a redirect to The Singularity Is Near. Here is a to how the page looked at 30 July 2011. It's probably best to simply remove the link from "errors" as the topic seems insufficiently sourced for a mention here. Johnuniq (talk) 22:00, 2 January 2012 (UTC)

mutation as mechanism of natural selection
The following quotation from the description is misleading: "Mutation is generally accepted by biologists as the mechanism by which natural selection acts, generating advantageous new traits that survive and multiply in offspring as well as disadvantageous traits, in less fit offspring, that tend to die out." Mutation is NOT the mechanism through which natural selection acts. Differential reproductive success is the mechanism; mutation is necessary in that it is the source of the variation, but it is definitely not the mechanism. To suggest so seems vaguely Lamarkian (i.e., Natural Selection somehow forces a mutation) — Preceding unsigned comment added by 198.161.51.7 (talk) 16:24, 17 February 2012 (UTC)
 * Good point. I changed it. Biosthmors (talk) 16:48, 17 February 2012 (UTC)

Changes to Beneficial Mutations Section
Hi guys, was wondering if the section on beneficial mutations can be edited to include something about natural selection, since along with the example cited, CC5R, this possible explanation accompanies it. "One possible explanation of the etiology of the relatively high frequency of CCR5-Δ32 in the European population is that it conferred resistance to the bubonic plague in mid-14th century Europe. People with this mutation were more likely to survive infection; thus its frequency in the population increased." Since this explanation is one of natural selection of the fitter, would it be fit (pun not intended) to add something about natural selection? — Preceding unsigned comment added by LimpSpider (talk • contribs) 09:01, 26 June 2012 (UTC)

Adding DNA
One thing I've been trying to figure out for a while: I know that mutations can sometimes be beneficial...but the question is, can they actually INCREASE THE LENGTH of DNA molecules? I looked online, and people say opposite things...are there scientist that have opinions on this?72.80.198.221 (talk) 18:02, 11 September 2013 (UTC)
 * Mutations can increase the length of DNA such as with gene duplication and transposable elements. Whether it is beneficial depends on the mutation. Telomere lengthening may prolong cell life (which may be beneficial, or harmful if its cancer). The insertion of transposable elements after a promoter could inactivate a gene. This article needs work.Fundon1 (talk) 03:25, 19 January 2014 (UTC)

Always inherited?
Could something be added into the first sentence of the introduction to clarify whether or not mutations are always inheritable? Genetically malformed individuals whose genetic malformation, for instance was the result of their mother's ingestion of thalidomide, do not I believe necessarily have similarly affected offspring. I raise the point as this article is referred to, as the primary source in another article here, as being one of the four primary sources of genetic change in pupulations. LookingGlass (talk) 08:16, 6 March 2014 (UTC)

Are mutations observable?
Can someone clarify this in relation to the page subject? Because this important point is not discussed at all. Are mutations directly observable (e.g. with a telescope) or are they inferred?

The following source says: "Here, the focus is on mutations that affect only single genes and are not microscopically observable." FossilMad (talk) 21:47, 5 June 2014 (UTC)
 * You would probably get a good answer at WP:Reference desk/Science. You might find Nylon-eating bacteria of interest. Johnuniq (talk) 00:45, 6 June 2014 (UTC)

Defective sentence
The section Somatic mutations includes the sentence "When analyzing somatic mutations present in the cells of multicellular organisms, can know its origin and its past."

Can someone fix this sentence? What is the subject of the verb "can know", please? And what is the antecedent of the pronoun "its"? Dirac66 (talk) 02:32, 1 July 2015 (UTC)

Assessment comment
Substituted at 00:40, 30 April 2016 (UTC)

"Novel Mutation" --> New Mutation
At several points, the article uses the term "novel mutation" to talk about new mutations, as opposed to inherited ones. The National Cancer Institute defines the term "novel mutation" as one that as been previously undiscovered/unreported, and scientific literature uses the term as such, while "new" or "de novo" mutations to refer to a mutation present in an organism that was not present in the parent. (Apologies for the drive-by flagging.) 199.217.4.94 (talk) 19:02, 22 August 2016 (UTC)

Mutation review
“By effect on protein sequence” mentions frameshift, nonsense, missense, neutral, and silent mutations, which were discussed in “By effect on structure.” Can these sections be combined?

"Replication timing quantitative trait loci affects DNA replication" does not mention how DNA replication is affected.
 * A good source found on the rtQTL Wikipedia page, relating to mutation types based on replication timing.

The final paragraph of the “Beneficial mutations” section lists sickle-cell disease as an example of a harmful mutation. I believe sickle-cell disease should be discussed in “Harmful mutations,” while the sickle-cell trait should be covered in “Beneficial mutations.”

Finally, I believe there needs to be more information related to how mutations are located and fixed within organisms. I.e., Photoreactivation repair, base excision repair, nucleotide excision repair, etc.

JJCim (talk) 22:25, 29 March 2017 (UTC)

Reorganized and clarified "By effect on structure" and "By impact on protein sequence" subsections
These two subsections were a complete mess, full of duplications and contradictions, and it was not clear how the content was divided between them. I have substantially revised their organization and nested the classifications in a way that I believe is more logical. Ted.tem.parker (talk) 03:30, 3 May 2018 (UTC)

Mutation Evaluation
I like how the article is organized. It covers many aspects related to mutation, so if anyone does not have an idea about mutation he is going to find all the sources. Another great thing about the article is that it describes a different kind of mutation, the causes and it provides links to other articles which would be helpful to the reader, also the article is well resourced.Halhamdan (talk) 20:13, 18 September 2018 (UTC)

Should "Classification of Types" be divided into multiple sections?
This is a currently really long section, with following subheadings:

3.1	By effect on structure (3.1.1	Small-scale mutations 3.1.2	Large-scale mutations) 3.2	By effect on function 3.3	By effect on fitness (3.3.1	Distribution of fitness effects) 3.4	By impact on protein sequence 3.5	By inheritance 3.6	Special classes 3.7	Nomenclature

Would it make sense to rearrange this into multiple sections? I think many of these are of more than enough importance to warrant it. HFHah (talk) 14:53, 22 April 2020 (UTC)

Unnecessary Addition
"In December 2017, the U.S. government lifted a temporary ban implemented in 2014 that banned federal funding for any new "gain-of-function" experiments that enhance pathogens "such as Avian influenza, SARS and the Middle East Respiratory Syndrome or MERS viruses."[47]"

This sentence from the paragraph on gain-of-function mutations is pretty obviously superfluous and intended to push some kind of political agenda. It should be removed. 2001:569:BD89:A00:1CB9:93A9:8DB7:FC21 (talk) 05:34, 4 May 2020 (UTC)

Somatic mutation, merge or split?
I believe somatic mutation warrants spin off into its own article. See Draft:Somatic mutation

Some reasons in favor of spin-off:
 * Somatic mutations have important and distinct traits/effects/roles from germline mutations and mutations as a whole.
 * Mutation is already a long article.
 * some evidence of notability: plug "somatic mutation" into google scholar and you get a whole lot of journal articles back - topics include: cancers (#1 by far), other diseases, mitochondrial mutations, healthy cell mutations.

These distinct issues include:
 * Rates of mutation [compared to germline, comparison between different somatic tissues, causes of different rates at molecular and evolutionary scale]
 * instances of inheritance (e.g. in plants, in some animals)
 * role in immune function (somatic hypermutation)
 * how many cells a mutation affects (e.g. did it occur early in development? did it occur in a post-mitotic cell or in a rapidly dividing cell?); general somatic mosaicism of tissues (especially somatic brain mosaicism).
 * accumulation of mutations: role in disease (well studied: cancer, maybe: neurodegenerative diseases), as potential cause of aging.
 * techniques used in research, e.g. single cell sequencing.

Downsides: Many of these topics have mention in other articles [in varying amounts of detail]; some could use further elaboration. Benefits to gathering information in one place to understand overarching role of somatic mutation?

HFHah (talk) 19:06, 13 May 2020 (UTC)


 * The draft looks OK to me, I see no issue with it being a separate article, the topic is notable enough. Splitting the article is fine, and not necessary to merge. Hzh (talk) 11:08, 14 September 2020 (UTC)]
 * If it is done, do we need the template anymore? Andrew Z. Colvin • Talk 19:23, 19 December 2020 (UTC)

Wikipedia article about "gain-of-function" experiments needed
A Wikipedia article about "gain-of-function" experiments, especially as regards viruses, is needed. The coverage in this article (which redirects from Gain of function) does not properly explain how such experiments are done, or for what purpose. Do any of the editors of this page have the knowledge and expertise to do this? 173.88.246.138 (talk) 21:38, 17 January 2021 (UTC)
 * Unfortunately, editorship is much lower than it used to be so if you have the expertise, consider writing an article or adding a section about the topic. Be sure to cite everything. If you need help, reach out! Andrew Z. Colvin • Talk 20:49, 19 January 2021 (UTC)

Wiki Education assignment: Molecular Genetics
— Assignment last updated by AndrewDunham14 (talk) 01:06, 10 October 2022 (UTC)

Action items
A list of things to do, following up on the review below Dabs (talk) 08:55, 10 March 2023 (UTC)


 * [ ] gather all info on types (subst, microindel, ins, del, duplication, etc) into one section after the Overview. This will be the main section of the article
 * [ ] integrate links to mechanisms and types of mutations described in more detail elsewhere
 * Gene duplication
 * Deletion_(genetics)
 * Chromosomal_translocation
 * Transposable_element
 * see links under Chromosome_abnormality
 * Microsatellite
 * Mutational signatures
 * [ ] add well documented examples of disease-causing mutations
 * [ ] add well documented examples of evolutionarily important mutations
 * [ ] add well documented examples of beneficial mutations in humans (e.g., HIV resistance) — Preceding unsigned comment added by Dabs (talk • contribs) 09:05, 10 March 2023 (UTC)
 * [X] delete redundant list of types (missense, nonsense, etc) under By Inheritance
 * [X] delete off-topic history section
 * [X] remove Darwin
 * [X] remove comment about gain-of-function research ban

Review prior to making some revisions
Below is my review of this article. I will make a list of major and minor suggestions and get to work on those presently Dabs (talk) 15:32, 9 March 2023 (UTC)

synopsis of review
This article has some bright spots but generally its a mess with a low content/length ratio. It often repeats basic knowledge found in other articles, and is full of statements that lack context. The organization and the topic headings often are not justified by the content. The history section is irrelevant and is copied from another wikipedia article.

Given the existence of other articles on Wikipedia, I think it would be smart to focus this article mainly on mutation as the genetic perturbation of a biological system, characterized by the structure of the change, and by its effects, with suitable examples given along the way, as distinct from (1) mutation as the mechanistic consequence of DNA replication and repair or (2) mutation as a process that contributes to evolution. That is, given a biological system with an inheritable component, there are some enumerable ways to change the inheritable component, and these have some known and unknown consequences to consider for this article.

Material to deconvolute or keep separate vis a vis other articles
 * shift the causation of mutations to mutagenesis and DNA repair
 * population genetics belongs in population genetics
 * other than a few examples, put genetic diseases in genetic disorder
 * other than some examples, put rates and biases in mutation rate and mutation bias

Material to integrate into target article
 * germline mutation

Material to carve off into a separate article
 * compensatory mutation

Lede

 * image of Darwin does not belong on this page
 * the choice of that 2007 study is idiosyncratic and does not belong here

Overview

 * missing: clear statement of scope of this article relative to others
 * missing: list of relevant problems or phenomena that have a close relationship to mutation, with links to Wikipedia, e.g., monogenic diseases, cancer, antibiotic resistance, forensic identification, evolution
 * general: overview mixes comments about types of mutations and categories of effect, without being clear about the distinction
 * immediately starts out with idiosyncratic point about duplications
 * irrelevant comments about gene families
 * second para, irrelevant comments about domains as modules
 * third para, good to raise chromosomal changes, but don't speculate about significance, that's out of scope for the overview
 * butterfly example seems idiosyncratic
 * comment about DNA repair is out of context
 * comment about beneficial mutations lacks context
 * red tulip with yellow petal: how do we know this reflects a mutation?
 * other flower is not named by species and again, how do we know this reflects a mutation?
 * why not use examples like albinism or melanism?

Causes

 * general: this is not well informed
 * general: IMHO the "causes" section should be brief and refer the reader to mutagenesis
 * this is a made-up categorization
 * it is not clear what "spontaneous" means here (it is not defined)
 * then it jumps to a 2017 study about cancer-causing mutations
 * then another statement about mutations passed on by humans, utterly out of context

Spontaneous mutation

 * this immediately confuses the scope by talking about damage
 * this is a hodge-podge, not a good categorization of spontaneous mutation, bc it refers to errors in DNA replication and 2 kinds of damage, after introducing the section by saying that the mutations can be categorized by type. What is offered is not a categorization by type, but by etiology.

Error-prone replication bypass (sub-heading of Causes)
 * not much here
 * should refer to main article DNA repair: Translesion synthesis

Errors introduced during DNA repair (sub-heading of Causes)
 * this obviously overlaps with the previous section, so that it is not clear why this is being treated separately
 * the comments focus on NHEJ rather than errors during repair generally

Induced mutation (sub-heading of Causes)
 * in the definition given, the reference to "environmental causes" makes this vague and broad: "Induced mutations are alterations in the gene after it has come in contact with mutagens and environmental causes."
 * the "highly regulated mutagenesis" comment is out of place here

Classification of types

 * general: finally we are getting to some useful material here
 * missing: begin by describing dimensions of diversity captured by a Classification
 * missing: introduction to this section

By effect on structure

 * are we talking about types of effects, or types of the structure of the mutation?
 * nice illustration of chromosomal changes, very useful
 * nice illustration of deletion, insertion, substitution in DNA sequence

By impact on protein sequence

 * the title is wrong: this is referring to parts of a gene, not just parts of a protein
 * this has some examples mixed in but inconsistently
 * confident speculation about neutrality of synonymous changes does not belong here

By effect on function

 * note that this is using Muller's terminology of neomorph, hypomorph, etc. inconsistently; see Muller's_morphs
 * comments about politics of bans on gain-of-function experiments are irrelevant here
 * examples are welcome but used inconsistently here

By effect on fitness (harmful, beneficial, neutral mutations)

 * don't put "neutral" in parentheses if it is one of the 3 main categories
 * what is the scope here?
 * there are lots of mistakes here and odd language that indicates a lack of familiarity with the material
 * "thousands of millions of mutations are tested". No, there are no experiments with so many mutations. The total number of all mutants from published DMS studies might be on the order of a million or a few million.
 * "earliest theoretical studies of the DFE was done by Motoo Kimura". No, that is not an accurate way to describe the neutral theory
 * talking about deep mutational scanning is a great idea, but it does not belong under fitness, which is only one of the measurements done on mutants. This deserves its own category
 * generally this material needs to be re-organized but it can include
 * classical mutation screens with transposons
 * DFE studies from Sanjuan and others
 * deep mutational scanning from the past 10 years
 * suggest retitling this section to "experimental mutation scanning" and including the above categories

By inheritance
Germline mutation.

Somatic mutation
 * the material included here is redundant to material above
 * this entire section can be deleted

Special classes

 * "conditional mutation" is not a term that I recognize. Obviously there are cases of conditional expression, but this seems like an application of basic genetic concepts rather than something specific to the concept of mutation
 * there are only 2 categories here, and the second one is empty, so this section can be deleted.

Nomenclature

 * this starts out with BS
 * I think that a short section on nomenclature is useful, but it belongs much closer to the top of the article
 * suggest to delete this section and inline the contents as appropriate

Mutation rates

 * repeats a numerically different version of an earlier claim about the number of novel mutations per human
 * comments about DNA vs. RNA are out of place
 * there is very little information here
 * suggest to delete this and refer to mutation rate repeatedly throughout article

Randomness of mutations

 * nothing necessary here

Disease causation

 * repeats comments from the lede about a drosophila study that are not germane here

Inherited disorders

 * repeats basic information on mutation without providing a broad substantive statement on the topic of inherited disorders

Role in carcinogenesis

 * repeats basic info about mutation ("Point mutations may arise from spontaneous mutations that occur during DNA replication.") without a substantive overview of the topic of carcinogenesis

Prion mutations

 * if mutations are changes to the genetic material, but prions are not genetic, then how can they be said to have mutations?
 * I know nothing about this but this concept does have sufficient literature support . — Invasive Spices (talk) 19:41, 9 March 2023 (UTC)
 * Yes, prions are real. The issue is how to describe them without confusing the reader or contradicting the definition given earlier in the article. In this case, one answer is that heredity in the case of prions is protein-mediated, so that a change in the protein can be considered as a kind of mutation.  Dabs (talk) 08:29, 10 March 2023 (UTC)

Beneficial mutations

 * nice, I like the idea of a section like this. In fact I think the article needs a section on some notable deleterious mutations, and another one on some notable beneficial mutations.

Compensated pathogenic deviations

 * this is an absolute mess. What does para 2 have to do with the topic of compensated pathogenic deviations?  This is just repeating concepts about population size and fitness.
 * "Therefore, any mutation that alters the stable structure of RNA molecules must be compensated by other compensatory mutations." Ugh, this is sophomoric logic.
 * "In the context of RNA, the sequence of the RNA can be considered as ' genotype' and the structure of the RNA can be considered as its 'phenotype'. " Why are we told this?
 * the existence of this section is not justified. It does not clearly and substantively add to the reader's knowledge of mutations.
 * clearly someone has done a lot of reading and digesting of papers on compensatory mutation. I would not want to just throw it out, but it does not seem to fit with the rest of this article, which is about a high-level topic.  Maybe it can be kept with the intention to eventually carve it off into a separate article that should be titled "compensatory mutation", which would also include Kimura's compensatory mutation model and perhaps a reference to stochastic tunneling.

History
Dabs (talk) 15:32, 9 March 2023 (UTC)
 * the dubious history in regard to "Mutationism" is not relevant
 * the text is largely repeated from another wikipedia article. I recognize all of this text.
 * there is no reason to repeat it here
 * an appropriate history section for this article would focus on the discovery and elucidation of the nature and causation of mutations, e.g., the first clear demo by de Vries and its replication by other scientists; systematic work on obtaining and mapping fly mutations by Morgan's group; the demonstration of the effect of radiation; Benzer's mapping of genetic fine structure; possibly McClintock's early work on maize instability.


 * I agree with just about every criticism that Dabs raises. This article is supposed to be about mutation but it has become contaminated with a lot of extraneous material that doesn't belong here - especially material that's covered in other Wikipedia articles.
 * There's also a lot of misinformation here, Nmitchell921 has just fixed the section on mutations rates but it shouldn't have taken several years. (Thank-you Nmitchell921.)
 * I don't think we should be describing evolution in this article. It's a complicated topic and we should be focused on making the main article (Evolution) as accurate and up-to-date as possible. It not a good idea to have conflicting views of evolution scattered throughout related articles on Wikipedia.
 * I think the section on "Distribution of fitness effects (DFE)" should also be removed and so should the section on "Nomenclature."
 * The section on "Randomness of mutations" raises some very controversial issues. It emphasizes a perspective that can be seen as very misleading. For example, the phase "biologically important regions were found to be protected from mutations and mutations beneficial to the studied plant were found to be more likely" is not a fair assessment of the scientific consensus.
 * The various sections on human diseases don't belong here because they are adequately covered elsewhere in articles that are far more accurate and comprehensive.
 * Removing material from an existing Wikipedia article is bound to create a lot of criticism from the Wikipedia editor community. Let's discuss it here. Please express your support if you agree that this article should be cleaned up. Genome42 (talk) 17:12, 10 December 2023 (UTC)