Talk:Mutagenesis

Wiki Education Foundation-supported course assignment

This article was the subject of a Wiki Education Foundation-supported course assignment, between 17 August 2020 and 2 December 2020. Further details are available on the course page. Student editor(s): Mmott2018.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 04:42, 17 January 2022 (UTC)

Initial comments

I would consider mutagenesis to be a special case of mutation --buzco

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The statement that mutagenesis is "the driving force of evolution." is a bit strong. IMHO, "is considered to be the driving ..." or even "is considered to be a driving ...". Consider genetic drift for instance. Also there are some (probably all or mostly all outside the citadel of Established Science) that are not at all sure that "evolution of species" is entirely mechanical or randomly driven.

BTW, the phrase evolution of species is more correct than the simple word evolution. Evolution of species is a special case. -- buzco

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I disagree that this article should be merged into Mutation. Mutagenesis should be considered as the methods in which to obtain specific mutations used in protein engineering. There are numerous different methods used in modern industry which would make up a lot of material for an article on its own. I'll start it up after I've worked out a system on the Swedish article on the same theme, but if someone want to start the article out, I'd be happy. Axelve 18:35, 28 September 2006 (UTC)

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I believe the two are seperate terms and each is deserving of its own article as each has differing relevances, though related, they're difference things, intrinsically. So, I agree with Axelve

--lincalinca 09:09, 18 October 2006 (UTC)

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I think it is probably worth giving mutagenesis its own page to cover the subtopic of how mutations arise, distinct from the mutation page which is mostly spent classifying mutation types.

I took the word "heritable" out of the definition since not all mutations are heritable e.g. cancer can be caused by somatic mutagenesis. —Preceding unsigned comment added by 194.171.7.39 (talk) 13:06, 2 March 2008 (UTC)

Six types, one defined here

The article lists six types of mutagenesis, with links to separate articles for all but the first one, which is defined here. This is a poor organization. I leave it to better informed editors on this subject to decide how to correct this situation. --DThomsen8 (talk) 13:33, 14 June 2009 (UTC)

Two complaints

Two complaints: First, "Targeted mutagenesis" redirects to "site-directed mutagenesis", so they probably shouldn't be listed as separate links. Not sure if this was a recent edit that no one noticed yet, but it's a little confusing. Second, someone said that this article should be incorporated into the article on mutation. I think it's good to have a separate article on mutagenesis as a scientific technique, in contrast to mutation as a general process, but we have to have it be more informative about the methodologies and perhaps have links to things like EMS and X-ray mutagenesis. It's kind of an important method in genetics, and deserves a better article. I'm a bio major, but I don't have the time to do it right now and i'm a bit of a noob on wikipedia editing. --AnonymousUser5 —Preceding unsigned comment added by AnonymousUser5 (talk • contribs) 04:32, 26 January 2010 (UTC)

I deleted the link to targeted mutagenesis (Is this the same thing as site-directed mutagenesis? The term isn't mentioned on that page.)

I don't know enough about this to expand the article myself. Perhaps you have time later on – you can ask for assistance with editing anytime, for example on my talk page or on Wikipedia talk:PHARM, or on Wikipedia:New contributors' help page. Or place {{help me}} on your talk page. Cheers --ἀνυπόδητος (talk) 17:40, 27 January 2010 (UTC)

I have created a separate page for mutagenesis as a laboratory technique in molecular biology in Mutagenesis (molecular biology). That page can be further expanded to give a more in-depth treatment of its use in molecular biology (it is one of the most important techniques in molecular biology), while this page will be reserved for the general process of mutagenesis where more details about the various mechanisms by which mutagenesis occurs can be added. Mutation and mutagenesis should also be kept separate because mutagenesis is an important subject on its own. Hzh (talk) 15:51, 28 May 2013 (UTC)

Review prior to making systematic revisions

My review of this article is below. I will suggest a list of major and minor revisions and begin on those later this spring Dabs (talk) 15:25, 9 March 2023 (UTC)I

Action items

• [] remove Darwin
• [] remove comments about bans on GoF research

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, and statement that are misleading or wrong. 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.

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?

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

• this is largely garbage history in regard to "Mutationism"
• 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; systematic work on obtaining and mapping 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.

Dabs (talk) 15:25, 9 March 2023 (UTC)