Talk:Mutation/Archive 1

Blue eye = beneficial mutation. Possible troll?
I dont usually edit wikipedia articles, so I'm hoping a good samaritan will do it for me. Under the beneficial mutation heading, there is blue eyes being listed. I believe this to be a subtle troll regarding Aryan race and Hitler, if it does confer a beneficial advantage (Blue eyes tied to the same locus as fair skin, fair skin required for Vitamin D production in lower sunlight areas) it should be edited in, otherwise it appears to be a subtle racist troll in wikipedia. It has a reference to look legit. Check in on it someone? — Preceding unsigned comment added by 120.144.0.1 (talk) 13:11, 30 August 2012 (UTC)

mutation "on purpose"
i seem to remember reading about a "subtheory" that says that certain mechanisms in cells encourage random mutation, or actually facilitate not-completely-random mutation under conditions of stress. is this nonsense? is it a real theory? is there a name for it?

i also seem to remember reading about a lizard or worm or something that disassembles parts of its dna and rearranges them every once in a while, which may be unrelated. - Omegatron 01:07, Sep 28, 2004 (UTC)

I think this is called directed mutation. The original paper on directed mutation was: Cairns, Overbaugh and Miller (1988), The Origin of Mutants, Nature 335: 142-145. --Heida Maria 20:45, 8 Mar 2005 (UTC)


 * This mutation "on purpose" you speak of is simply an accelerated form of this random mutation, which seems to be encouraged by stress situations, in a last attempt to survive. This seems to be directed mutation because the unsuccesful and negative results of this mutation are lost as these cells in which they result are less succesful. In a similar manner evolution often seems to be directed to result in a certain manner, this is simply a result of the extinction of unsuccessful organisms. Tuganax 06:27, 18 May 2007 (UTC)

Additionally, many evolutionary biologist don't think that directed mutations or adaptive hyper-mutation (i.g. Mike Lynch and well, me.) exist (with the exception of somatic hyper-mutation), though there is some debate about the issue. I could certainly see including a section on this. Matthew Ackerman (talk)

Insertion picture
The picture is slightly misleading in its illustration of insertion mutation. Insertion means that a sequence is inserted (rather obviously) in a chromosome. The concept is not constrained to the process where the sequence is lost (deletion) at its place of origin. Rather it is more common that the inserted sequence is a copy of an origin that is left intact. The picture shows the origin being deleted (at the origin). Etxrge 20:35, 29 Dec 2004 (UTC)

Actually I am very unsure which is the most common. Either way, the picture shows the behaviour of a transposon, which is only one of the causes of insertion mutations. /Etxrge 12:01, 31 Dec 2004 (UTC)

Mutation
I wonder, does mutation occur randomly or is it controlled by rules? Can you predict when a mutation would occur in an organism or species or is it all random? As you can see I am not a biologist in any way whatsoever. I thought of my question while reading the article on memes. Jaberwocky6669 09:59, Jan 2, 2005 (UTC)

Well, the answer to "Can you predict when a mutation would occur in an organism " is yes and no.

We know, for instance, that thymine dimers on a DNA strand (that is to say, a sequence of TT), are susceptible to "buckle" under UV light and cause a mutation. At the same time, most other mutations occur randomly, as a result of both environmental changes and also mobile DNA like transposons, retrotransposons, SNPs, LINEs, SINEs, etc jumping in the middle of a gene to disrupt it.

Are the rates of mutations (per amount of DNA/RNA) basically static among all organisms? Or have different organisms evolved different structural techniques in making them less/more likely to happen? Peoplesunionpro 01:45, July 20, 2005 (UTC)

First sentence - "Mutations are permanent" is not qualified until the end of the paragraph where DNA repair is mentioned. How about simply dropping the "permanent" until it is necessary to mention.

Chromosome mutations?
My opinion is that there should be two distinct articles for mutations on DNA level and chromosome mutations. These are two very different things, and also words like 'insertion' and 'deletion' are used in both types of mutations, but the size of the regions differ enormously ('deletion' at DNA level typically means 1-3 base pairs, but at chromosome level it means like 100000+ bp). The illustration is about chromosome mutations, and is confusing since most of this article is about DNA level mutations. Also, there is currenctly nothing about the functional classification of mutations in this article, and I certainly think there should be. I will try to add some of this now.
 * Hi I saw your good changes. My recommendation is just get stuck in.  I have seen quite a few mistakes in the biology related sections. You have only seen the tip of the iceberg. By the way welcome to wikipedia if you are new.  David D. 21:49, 25 July 2005 (UTC)
 * The following was on my to do list but go ahead since this seems to be an area you are familiar with feel free to take over (Hypomorphic mutation and mutation merge adding in hypermorph antimorph etc.).  Sorry for taking advantage of your enthusiasum ;-) David D. 21:54, 25 July 2005 (UTC)

Supporting Evidence Missing
The page states more or less as a mater of fact this: ''Mutations are considered the driving force of evolution, where less favorable (or deleterious) mutations are removed from the gene pool by natural selection, while more favorable (or beneficial) ones tend to accumulate. Neutral mutations do not affect the organism's chances of survival in its natural environment and can accumulate over time, which might result in what is known as punctuated equilibrium, the modern interpretation of classic evolutionary theory.'' Is there any solid evidence for this (if so please include it) or is this just fancy hand-waving? Madiuq 23:13, 28 September 2005 (UTC)
 * In reply to your quote "Is there any solid evidence for this (if so please include it) or is this just fancy hand-waving?", what hand waving? There is a clear reference to natural selection.  Why is that not acceptable? David D. (Talk) 23:42, 12 November 2005 (UTC)

You could start with the wikipedia Natural selection. If you prefer scholarly papers there are thousands. try these for examples of neutral and positive selection. Are you suggesting that specific examples be cited or that links to other wikipedia pages be incorporated? David D. (Talk) 04:16, 29 September 2005 (UTC)

Both would do. Right now it just stands there, preaching to the converted, not really explaining or proving what it claims. It would be nice if this article could point to a experiment where one could see an improvement which carried on to it's offspring.

Just some personal background: I am a computer scientist and the concept of random mutations sounds like signal noise. The idear that "noise" could improve on the programming is non trivial and should imho therefor be proven, not just stated in a mater of fact way like it is. Madiuq 23:02, 29 September 2005 (UTC)


 * As a computer scientist you will find the following link interesting (genetic programming). The point you are missing is the selection. You are correct that mutations are similar to noise.  However, due to selection, only the useful noise is preserved. Engineers and computer programmers use the noise/selection process too, and it works . David D. (Talk) 16:43, 16 October 2005 (UTC)


 * I know this, I also know that this useful noise does not accumulate under the conditions stated here. In genetic programming a signal will adapt to match the predefined test, finding an (often local) equilibrium between adding noise and loosing noise. At this point at higher levels the signal will seem to be stable and unchanging (sometimes going to a short cycle).


 * However, If at this point the test is changed, it will again search for a new equilibrium and loose all the information of the previous test. No accumulation between tests.


 * Also, the selection process defines, as a casting mould, the outcome between very narrow boundaries. In genetic programming the selection process (the predefined test) introduces a lot of information. Genetic programing has very little to do with my question, You're comparing apples and oranges.


 * Without a (very good) predefined test, genetic programming will produce just random noise. This is not a problem because nobody is using genetic programming in that way; There is always a goal.


 * I ask for evidence that beneficial mutation do accumulate. -- Madiuq 23:02, 9 November 2005 (UTC)
 * First it depends how you define benificial. Make better or help survive? Isn't the test life (natural selection)?  When industrialists use molecular evolution to make new heat and low pH stable proteins (the biological component of washing powders) this does not entail losing all the information from the previous test but building on it. And yes some may be lost, but not if it's useful. Every iteration is NOT starting from scratch as you seem to imply for your example above.  What is your problem with natural selection again, I'm still a bit fuzzy on what you find incorrect about that concept? David D. (Talk) 15:16, 10 November 2005 (UTC)


 * The difference, I believe, is that in genetic programming the definition of 'favourable aspect' is fixed(in conventional cases of gen. programming anyway), in evolution it is dependent on the environment. Generally a 'favourable aspect' is one that allows its bearer to spread it, the most usual cases being increased chance to survive and increased chance to mate. Both of these are dependant on the environment however, so they are not fixed. Also see under natural selection why some consider it to be a tautology.


 * The chromatic spectrum of butterflies is generally very varied. It is a favorited form of evolutionary demonstration. That sentence is simply giving a text book example on genetic mutations. —Preceding unsigned comment added by 216.128.93.23 (talk) 23:41, 7 October 2009 (UTC)


 * Something else I did read was that there has been no proof of benefitical additions, the only kind of benefitical mutations has been a loss of genetic information. It was a Creasionist website though, so it's probably used in a different context. --Dyss 21:10, 10 November 2005 (UTC)
 * I would not trust the information you get from a creationist web site with regard to biology. The creationist position is that you cannot increase information, or create new information that is beneficial to an organism. The problem is they are wrong. There are many examples of gene duplication and genome duplication such that two genes are created with redundant function. Changes in the second genes function can allow an organism to acquire a new and possibly beneficial function. This could occur by changing the sequence the gene OR changing the temporal expression of the gene OR by changing the tissue specific expression of the gene.David D. (Talk) 21:30, 10 November 2005 (UTC)
 * Yeah, I take Creationism biology with a grain of salt, though the site looked rather sane for it. According to them
 * ...we should say, ‘We have yet to find a mutation that increases genetic information, even in those rare instances where the mutation confers an advantage.’ (http://www.answersingenesis.org/home/area/faq/dont_use.asp)
 * and
 * A group of creatures might become more adapted to the cold, for example, by the elimination of those which don’t carry enough of the genetic information to make thick fur. But that doesn’t explain the origin of the information to make thick fur.(http://www.answersingenesis.org/creation/v19/i3/beetle.asp)
 * I thought that maybe Madiuq was referring to this, though the site is probably lying or putting things in a way to promote Creationism. --Dyss 22:19, 10 November 2005 (UTC)

Dudes, this is a basic principle of the theory of evolution, surely there is some simple way to demonstrate that it is true or at least reasonable to assume it to be true?

Genetic programming usually only operates over data, the basic functions (code) are assumed to be available as building stones from which to build. For biological systems the big question is not about data, but the origen of the code (software, programing).

I have done some experiments with genetic programming and I have found that, if anything, natural selection is very effective in (1) selecting an optional configuration (by tweaking data) that suits the current environment, and (2) in eliminating all mutations in the functional information (code). (Maybe I'll write a paper about this next year).

Notice that there is a huge difference between these two: A change in some data will only change the workings of the code that operates over it, where-as a change in the code will change not only the working of this code, but also the meaning (semantics, interpretation) of all the data it is operating over. This has a HUGE impact, and it's not beneficial.

To see any accumulative effects (like you describe) one needs to carefully design a stable code base and a test set, both of which are however outside the system and therefor irrelevant to this discussion: One would then in fact be providing evidence for the ID camp and I don't think you want to do that. I often hear genetic programming as an argument but the fact is that genetic programming is much more programming, then genetics.

Notice however that these are only simulations. They proof nothing about biology. I needed to make a few assumptions which may or may not hold for biological system. All I can say is that if it works in biological system then it's likely that there must be more at work then only mutations and natural selection.


 * Well what about the invitro protein evolution I mentioned above to develop protein for washing powders. They make proteins with a new function by selecting new variants from a pool of proteins with random mutations. Obviously depending on whether you select for protein variants that function better at low pH or high temp or both will change the 'beneficial' mutations that are selected. Did you look into that? If not here is a link to start you off . Why is this type of example no good for you?


 * Again, I have to ask what do you mean by "beneficial" mutation. In your computing analogy you seem to be focusing on mutations that break the function of the program. Well obviously they will not be selected in your programming example or in biology.  However, in biology you can make many mutations that have either a small detrimental effect or have no detrimental effect under a given environement (is that not true for computer programming?).  Once you start changing the environment (test in your analogy) such mutations may be selected (benificial under those test conditions) and accumulate due to giving the organism an advantage.


 * What about all the references in the literature that I cited above did you read any of those? What exactly do you want? Consider sickle cell anemia. Specifically the following paragraph from that wiki page:
 * "The sufferers of the illness have a reduced life span. It is believed that carriers (sickle cell trait) are relatively resistant to malaria. Since the gene is incompletely recessive, carriers have a few sickle red blood cells at all times, not enough to cause symptoms, but enough to give resistance to malaria.  Because of this, heterozygotes have a higher fitness than either of the homozygotes.  This is known as heterozygote advantage."
 * Why is the allele that causes that disease maintained in some populations? It is not beneficial in the sense you are using for your genetic programming.  However, it is beneficial in countries with high levels of malaria. Again, beneficial does not mean better in all conditions.  You yourself said above:
 * "In genetic programming a signal will adapt to match the predefined test, finding an (often local) equilibrium between adding noise and loosing noise. At this point at higher levels the signal will seem to be stable and unchanging (sometimes going to a short cycle). However, If at this point the test is changed, it will again search for a new equilibrium"
 * And this is the whole point, evolution is the same. The test is the environment and of course the environment is always changing.  Changing the environment will result in certain alleles either accumulating or not.  In the above example the sickle cell anemia mutation accumulates in populations where malaria is common.
 * Populations can be purged by a virus such that only those resistant to the virus will survive. Consequently, the random mutation that happened to confer resistance is suddenly more prolific in the population.  This happened in the North Sea to the harbor seal population when avian flu switched hosts and killed a huge number of the seals . The resistance allele may have not been particularly beneficial under 'normal' circumstances but when the virus became part of the environment those seals had a significant advantage.


 * You also say after the quote above:
 * "and loose all the information of the previous test"


 * In biology the population does not just lose all its information because a test changes. ALL the alleles (mutations) are still present in the population. Actually I don't see how you lose all your information in your anaolgy either, although this is probably due to my ignorance of computer programming.David D. (Talk) 17:11, 11 November 2005 (UTC)

But, I gather, that no-one has found a simple way to demonstrate this (very basic) principle? So this assumption is just that, an working assumption, and not really a proven fact. This does not have to be a bad thing, if the rest of the theory works then that will provide support for the assumption. Science isn't only about facts, sometimes we need to go beyond the evidence to solve the problem, sometimes we need to wait beter tools look at the assumptions once more. -- Madiuq 07:09, 11 November 2005 (UTC)


 * Yes, beneficial mutations can accumulate, because real environments are not absolutely uniform, and performance even under "uniform" conditions can produce multiple stable states. Lenski's E. coli experiment produces balancing polymorphism in a population originating from a single clone.  Two morphologically and physiologically distinct forms co-exist over many thousands of generations in a "uniform" medium.
 * While mutation occurs in individuals, evolution occurs in populations. If they are sexually reproducing, they can trade genes, they can mix and match their collection of neutral (or even mildly deleterious) mutations.  The difference between a simulation and the real world is two-fold.  One is inertia - individual A might have a mildly deleterious mutation in gene A, individual B might have a mildly deleterious mutation in gene B.  A might beat a and B might beat b, but A + b might be no better than a + B.  Granted, A + B is better, and a + b is worse, but the rate of elimination may be extremely slow.  If once ever 50 years you get a severe drought, and a + b is actually better than A + B in that one drought year, both mildly deleterious genes may do fine in the population.
 * Another thing to bear in mind is that it isn't genes that really matter, it's gene interactions. And multiple genes tends to mean redundancies.  Since genes X and Y essentially do the same thing, but X does it better, Y is free to "wander" mutationally without causing the plant any real harm...in essence, it is freed from selection, so it can go through some majorly deleterious intermediates before becoming useful for something altogether different (at which time it suddenly becomes "visible" again the natural selection.  Guettarda 07:41, 11 November 2005 (UTC)


 * Thank you very much. You're right to point out the scale difference between individual/population, maybe this is a situation where More is Different (Philip W. Anderson). I will look into it, and if needed (and posible) adapt my model. There are however a lot of "may"s in your reply which don't give me much confidence. -- Madiuq 11:20, 11 November 2005 (UTC)

Please remove the example of a butterfly having a beneficial mutation, unless you can provide specific evidence for it. Also, please provide specific evidence for beneficial mutations. Sickle cell anemia is about the only thing that has been cited in this discussion, as a possibility beneficial mutation, but it is just speculation. Additionally, no evidence for new genetic material has been cited. All that has been cited is either adaptation of old material, or deletion of old material. In order for this theory of good mutations accumulating to prove correct there must be evidence of new genetic material. So, please provide some specific evidence, or remove the speculation that mutations provide beneficial changes. —Preceding unsigned comment added by 216.163.247.1 (talk) 04:40, 6 October 2007 (UTC)


 * To explain a concept a hypothetical example is perfectly adequate, and therefore I consider your request for evidence to be irrelevant. Additionally it is not pure speculation - the possibility of such a mutation in a butterfly is supported by observations of industrial melanism in moths. (For all I know there may be equivalent observations in butterflies.) Lavateraguy 07:06, 6 October 2007 (UTC)

Punctuated Equilibrium
I changed a sentence of the first paragraph from "which might result in what is known as punctuated equilibrium, the modern interpretation of classic evolutionary theory." to "which might result in what is known as punctuated equilibrium, a disputed interpretation of the fossil record."

For one thing puncuated equilibrium is not an interpretation of classic evolutionary biology, it is an interpretation of the fossil record, which some have explained with theories. But most importantly puncuated equilibrium has not been ubiquituously (or even near ubiquitously) accepted by the biological science community. The most famous critic of the theory is Richard Dawkins of course. But he is in no way alone. I think my change conforms more to NPOV policy since puncuated equilibrium rates as a controversial theory among the biological science community.--Brentt 01:43, 16 October 2005 (UTC)

ATCG nucleotides?
In smallscale mutations, is the 'nucleotide' substitutes/added/substracted? I believe these are bases. Of course the entire nucleotide is wrongly copied (I assume ribosomes parses gen. material by the nucleotides into a peptide), but is there such a thing as a ATCG nucleotide? in my biology book they talk about ATCG bases, but they might have simplified it. Im only at late highschool level :) --Dyss 16:14, 7 November 2005 (UTC)
 * There are four nucleotides (or bases) in the nucleic acid. They are ATC and G. Each amino acid residue in a protein is coded for by three nucleotides that make up one codon.  David D. (Talk) 16:26, 7 November 2005 (UTC)
 * According to my book, a nucleotide consists of a nitrogen base, a fosfate group and a desoxybrose. I'm not sure if this is correct, but it's probably irrelevant to the article anyway and has more sense when looking in a smaller scale of dna. --Dyss 16:51, 7 November 2005 (UTC)
 * That is correct. So one nucleotide has one base. With regard to the discussion of mutations it matters not whether you discuss bases or nucleotides.  You are correct that this is very different when you start discussing the structure of DNA. David D. (Talk) 17:34, 7 November 2005 (UTC)
 * That's what I thought :) Thanks. --Dyss 18:12, 7 November 2005 (UTC)

Missing data
I believe one or more important types of biological mutation are missing from this article. See Horizontal gene transfer, Antigenic shift (important in current H5N1 avian flu problem), Reassortment. WAS 4.250 22:34, 28 November 2005 (UTC)

Mutation Hotspots
5-methyl-cytosine (5mC) is not a mutation "hotspot". 5mC is a modified base associated with epigenetics and gene regulation in eukaryotes. Deamination (a chemical process) of 5mC changes cytosine to thymine (T).

Seymour Benzer did find that there are mutational hotspots in bacterial viruses, and used this study to propose a model for gene structure. 128.32.3.26 05:05, 15 December 2005 (UTC) Anonymous, 12/14/05

Mutation and disease
The section Mutation and disease is too centered on mutations that cause changes in protein sequences. There are now many known disease-causing mutations that do not alter the sequence of any protein. Recent example: A common sex-dependent mutation in a RET enhancer underlies Hirschsprung disease risk. --JWSchmidt 13:42, 20 December 2005 (UTC)

Errors ID'd by Nature, to correct
The results of what exactly Nature suggested should be corrected is out... italicize each bullet point once you make the correction. -- user:zanimum


 * “Neutral mutations do not affect the organism's chances of survival in its natural environment and can accumulate over time, which might result in what is known as punctuated equilibrium, a disputed interpretation of the fossil record.” Evolution at DNA sequence and phenotypic level have been seriously confused here.
 * “+ silent mutations: codes for the same amino acid, so has no effect”: “so” not justified; a silent mutation could e.g. affect the splicing and if so, could even be lethal.
 * “; C → U, or A → HX (hypoxanthine).” This is not the full story, because e.g. a U in DNA would be recognized by the cell’s repair system and eliminated. But now the U pairs with A … (imagine replication). Or, the C is methylated, then you could get mC à T indeed.
 * “There are three kinds of point mutations, depending upon what the erroneous codon codes for:” This applies only to coding regions (open reading frames), but only a very small fraction of e.g. the human genome represents coding regions.
 * “Most insertions in a gene can either alter splicing of the mRNA, or cause a shift in the reading frame (frameshift),” How do the authors get to the “most”; my feeling is that this is not correct. The statement may also depend on the definition and composition of a gene; e.g., if it has large introns, it might be quite robust towards insertions or deletions.
 * “* Loss-of-function mutations are the result of the protein encoded by the gene having less or no function.” Genes encoding only RNA, or nothing, can also lose their function.


 * These seem all to have been corrected as of 26 December 2005. If you don't agree, please comment at External_peer_review/Nature_December_2005/Errors. - Nunh-huh 00:46, 27 December 2005 (UTC)

These errors stem predomiantly from the restricted view of mutations as only affecting the coding regions of protein coding genes. These regions make up only a tiny fraction of mammalian genomes, and thus most mutations are actually not of these kinds. We need to also mention that mutations can affect transcritptional levels, mRNA splicing, mRNA stability, etc. --Rikurzhen 17:03, 23 December 2005 (UTC)
 * At present it's a mixed bag and these errors are not consistent throughout the article. For example:
 * Hypomorphic mutations are mutations that cause reduced function of the gene product, or a negative change in expression of the gene.
 * Hypermorphic mutations are the opposite of hypomorphic mutations; they cause increased activity or expression of the gene product.
 * Neomorphic mutations cause a novel molecular function or expression of the gene product.
 * These definitions are quite clear and are not presumming loss of protein function as the only cause of the phenotype. David D. (Talk) 17:23, 23 December 2005 (UTC)

first paragraph: mutations permanent?
The first paragraph of the article contradicts itself. It starts by saying that "mutations are permanent" and ends by saying that "the overwhelming majority of mutations have no significant effect..... since DNA repair is able to reverse most changes before they become permanent mutations." --JWSchmidt 22:24, 25 December 2005 (UTC)


 * JWSchmidt, thanks for the comment. I think the problem is that there is no jargon available for distinguishing permanent mutations from those that are eliminated by various mechanisms (DNA repair, cell policing). My thinking now is that "permanent" in the first sentence is redundant. - Samsara 21:30, 6 January 2006 (UTC)


 * No it's not redundant, it's correct. It's proper to say that "not all changes in the genetic material result in mutation because there are many repair systems, etc". The part that needs to be edited is - Contrary to tales of science fiction, the overwhelming majority of mutations have no significant effect, since DNA repair is able to revert most changes before they become permanent mutations, and many organisms have mechanisms for eliminating otherwise permanently mutated somatic cells. "Mutation"="permanent change of the genetic material", not every such change result in a mutation, so "mutation" and "any change [ (both those that are permanent)=mutaions; and those that have been repaired ] of the genetic material" can't be substituted one for another. Mutations occur either because a replication cycle has occured before the repair of the damaged region could have taken place, or because the repair system has repaired the "good" strand (or chromosome), instead of the "bad" one. A question - what else beside DNA or RNA could be called a genetic material, as sentence number one suggests - In biology, mutations are changes to the genetic material (usually DNA or RNA) - ? -- Boris 23:39, 6 January 2006 (UTC)


 * As best I can tell, someone seems to have been thinking that prions have "genetic material" that is not RNA or DNA. See this comment. This needs to be fixed. --JWSchmidt 23:55, 6 January 2006 (UTC)


 * The meaning of the word "mutation" varys by context. In talking about individuals as in "That organism is a mutation" it means one thing. In the context of species it means permanant. In the context of molecules, it refers to the process or specific incidents or categories of incidents and "permanant" does not apply. WAS 4.250 00:57, 7 January 2006 (UTC)

Mutations without phenotype
A recent edit added this definition to the first paragraph "In genetics, the word mutation refers to either a change in the genetic material "of an organism resulting in the creation of a new character or trait not found in the parental type" or the process by which such a change occurs." this seems too restrictive. It implies that all mutations have a phenotype. the moilecular genetic defintion of mutation does not imply this. Is this definition from genetics era prior the the knowledge of silent mutations and DNA? David D. (Talk) 02:14, 26 December 2005 (UTC)

Oxidative damage is an induced mutation?
I may not be an expert, but according to my notes that I have, oxidative damage is a spontaneous mutation. It results from spontaneous lesions, in which oxidative damage will result in transversion mutation. Can anyone please clarify?

Sport
I've added a note to Mutant mentioning the word sport, as a more general term than mutant. If anyone has anything to add, feel free! Waitak 02:13, 29 September 2006 (UTC)

evowiki unreachable
nslookup evowiki.org same for www.
 * rns00.ka.rz-ip.net can't find evowiki.org: Non-existent host/domain
 * rns00.ka.rz-ip.net can't find www.evowiki.org: Non-existent host/domain

Whois still gives result

I removed the external link until it's up again Sancassania 14.10.2006 14.17 GMT Mutation is just somthing turned into a diffrent thing ohter then what it is. Example a person tuning into a snake is mutation.

Please don't spam.Goodone121 (talk) 22:11, 17 March 2008 (UTC)

Complicated
This article is awfully complicated. Dont you think it would be better to at least have a simple lead, or an Introduction to mutation ?--Filll 16:08, 9 January 2007 (UTC)

I agree. It reads as if written by a combination of laypersons vaguely familiar with the topic and biologists whose interests are peripherally related; it's surprisingly muddled and inexpertly explained for such an important topic. Moreover, changes in RNA are also mutations, so the very first sentence is imprecise. Why not just stick to "genetic material" and narrow in from there? (173.165.56.246 (talk) 03:49, 19 June 2010 (UTC))

Merging with mutation type articles
The are various small articles on particular kinds of mutations. Not so useful in isolation, and it would be more useful for readers of the mutation article to have that information in that article. It would also keep everything in the same style, more consistent, etc. --Frank Lofaro Jr. 19:22, 2 February 2007 (UTC)
 * I think it's a good idea to merge these in here. Most of the other articles are rather short stubs anyway. Alternatively, this one could have an introduction/overview and then short paragraphs on each mutation type with links to the other articles as main articles. Many of them should then be expanded though. - tameeria 17:59, 6 May 2007 (UTC)
 * I agree with Tameeria's latter alternative. The "mutation" article is quite long enough and is necessarily complicated. Visitors with particular interest in details of the various mutation classes can readily follow a link. These details are themselves worthy of considerable exposition and deserve expansion way beyond stubbiness. Myron 16:32, 20 June 2007 (UTC)

I disagree with the merge proposal, this should be a starting article, summarising the topic, but not trying to encompass everything on it. Perhaps an article entitled "types of genetic mutation" could be created, and merge them there? — Jack · talk · 15:04, Saturday, 23 June 2007
 * I agree with the merge. I think there should be a section on the classification of mutations by their effect (silent, neutral, deleterious, beneficial mutations, et cetera...). But I really don't see the point of having a whole article devoted to neutral mutations, it's quite absurd to have "Beneficial mutations" included in the main article, but neutral mutations are not. - PhDP (talk) 14:24, 12 July 2007 (UTC)
 * I support merging into types of mutation or classification of mutations. Even if this is a large article, it doesn't mean we have to go to very small articles if there is a theme in common. Richard001 02:44, 29 July 2007 (UTC)
 * I oppose merging adaptive mutation. Lavateraguy 11:47, 29 July 2007 (UTC)
 * I've added frameshift mutation to the list of candidates for merging, as it would seem to make sense to treat it in the same way as, e.g. point mutations. However I lean towards keeping separate articles for these, as for other types of mutation, such as duplication, deletion, inversion, translocation, monosomy, trisomy, etc. Lavateraguy 15:56, 29 July 2007 (UTC)

Merge from Mutant
Embarrassing article on a cultural neologism that attempts to find scientific merit. Little covered there that isn't covered in mutation, only here it's done better. Large overlap. Merge - Jack · talk · 12:15, Monday, 26 February 2007
 * Support so long as the difference between a mutant and a mutation is made clear. Dr d12 02:06, 27 February 2007 (UTC)
 * Support so long as the difference between a mutant and a mutation is made clear. Dr d12 02:06, 27 February 2007 (UTC)


 * 'Keep As Is. The distiction between the process and its product is pretty clear. Noclevername 21:33, 11 March 2007 (UTC) P.S. Why do you call a word that's been in common use for over a century a "neologism"? Noclevername


 * Moderately Oppose While the mutant article could use some improvement, I feel the distinction is valid -- in particular, the popular culture usage of the word deserves mention on the "mutant" page (although it's not there now). This information would look out-of-place on the "mutation page". Regarding "neologism" -- according to the OED, the word "mutant" arose in 1901, the same year as the word "mutation" was first recorded to be used in the biological sense. -Madeleine 14:16, 16 March 2007 (UTC)
 * No opinion now - I hadn't noticed there was a fictional article when I wrote this. I'm neutral on this idea now. Madeleine 00:02, 23 May 2007 (UTC)


 * Keep the two separate. In contrast to the multitude of mutation type articles which are just subtopics of this one, "mutant" has a clearer distinction as being the product of the mutation process. Also, it is highly ambiguous. If merging, I would suggest to merge the content of mutant here and then redirect that page to mutant (disambiguation). That might be the least confusing for users who might be more familiar with the popular culture use of the term than the scientific explanantion. - tameeria 18:10, 6 May 2007 (UTC)


 * Keep - Silent mutations are most likely going to play a very big role in research in the future. The recent work done on MDR1 and codon misuse, in particular, has me very interested. Zab 03:24, 17 May 2007 (UTC)

Mutations do not result in evolutionary change!
In the article, it basically states that: all you get as a result of mutation is just a varied form of an already-existing gene, i.e., variation within kind. This is correct of course.

However, mutations produce only alleles, which means they can produce only variation within kind, not change from one kind to others - which is evolutionary change. How then do mutations cause evolutionary change? --Lossenhilien 05:31, 19 April 2007 (UTC)


 * Mutations of gene duplication result in multiple copies of a given gene -- not alleles on different chromosomes, but an actual redundancy upon the same chromosome. Those duplicates are now freed to diverge in function through mutations in their respective sequences.


 * A nice recent example of this is the recent duplication of opsin in old world monkeys. This duplication of an opsin gene created two genes that were allowed to diverge in their response to light; the two genes in humans are now responsible for red/green color vision. See: http://www.genome.org/cgi/content/full/9/7/629, in particular this diagram: http://www.genome.org/cgi/content/full/9/7/629/F7. The two genes are LW opsin (long wavelength, in "red" cones) and MW opsin (medium wavelength, in "green" cones). Most mammals only have one gene here, a single "L/M opsin", and so are not able to distinguish red and green as humans do.


 * Because the duplication is so recent, the sequences in the region are still very similar and prone to misalignment during chromosomal crossover, resulting in a variety of mutations that can delete a gene, duplicate, or even create a fused gene which is half one gene and half the other. These mutations result in the various types of red-green color blindness, common in males because only have one copy of the genes (as they are on the X chromosome) -- protanopia (only the "green" opsin), deuteranopia (only the "red" opsin), protanomaly and deuteranomaly ("reddish green" and "greenish red" chimeric genes). -- Madeleine 10:47, 19 April 2007 (UTC)

Ok, I see your point, but you are referring to duplication, deletion and fusion. There is no extra information added, it is only rearranging it, even thought it is beneficial. The mutation hasn't added any new information, and the old world monkey is still within the same kind. --Lossenhilien 07:12, 20 April 2007 (UTC)
 * That is a classic creationist argument, and does not represent scientific opinion at this point of time. Therefore, with respect, it is irrelevant to this article. --Michael Johnson 07:16, 20 April 2007 (UTC)

Of course a mutation does not "result" in evolutionary change. It affects only a single instantiation of a species. It adds to the "gene pool" of that species. The new allele can potentially become increasingly common within a population and eventually become officially defined as the norm for that species, which, I suppose, is what is meant here by "evolutionary change". But this process involves transmission of the allele, expansion into the population over successive generations because of enhanced fitness, and official recognition by a human group... that's quite a stretch from the mutation itself "resulting" in evolution. Myron 16:26, 20 June 2007 (UTC)


 * This view is Platonic - the writer is looking as species as true forms, and at mutation as 'noise' or variation about that form. Although this view is not correct, it's unlikely any amount of evidence will convince them otherwise. Richard001 03:00, 21 July 2007 (UTC)

Stating that "That is a classic creationist argument, and does not represent scientific opinion at this point of time . . . . . " is not an answer to Lossenhilien. It merely excludes an argument that one finds troubling to answer. . . in this context anyway. " . . . and does not represent scientific opinion at this point of time . .  (so) is irrelevant to this article." implies that the writer is in total aware of what "scientific opinion" is at this time and any argument that is not in line with that opinion is not relevant is a critical mistake in logic and argument. Science as I learned it is open to any idea and through observation of empirical facts and demonstration one can decide on what is most probably true. Observation and theory compose science. . . not opinion. I would be much more helpful and respectful if the point being made was addressed rather than dismissed.

Labeling an argument a "classic creationist argument, . . . " I find disrespectful. Too often dialog is stopped short with such a remark. When one says such and such an argument is a "classic creationist argument, . . ." in my mind the writer might as well say "I'm too lazy and am tired of arguing over that issue so I'm just not going to." If I were a believer in creationist theory, and I do not admit to that, I would expect a reasoned answer to a hard question. If I were a believer in current evolutionary theory, I would expect those who speak as if they are full of authority to fully speak to any issue. And I would find it embarrassing to my position if I saw fellow evolutionary supporters respond as above and which I see more and more. . . the quick dismissing of an argument with such a statement as " . . . the objection by creationists to evolution by raising the Irreducible Structure argument has been completely debunked." I respectfully submit that those statements diminish science.

Finally, as one who will not "take either side," but values vigorous well reasoned arguments, such statements as " . . . it's unlikely any amount of evidence will convince them otherwise." is once again counter-productive. It reduces the apposed argument to dogma,. . . which I see no trace of in the argument being dismissed here. From much argument that I have heard and read from ardent evolutionist, I believe that dogma might be equally applied at certain times to the way men/women of science approach this issue.

In my opinion, science has never been dismissive but open to argument, and new information. The slow seemingly irresistible movement which I see to the view that science is fact, and from which the truthfulness of all else can be judged, is extremely troubling, especially when science is used as an excuse to dismiss without elaboration].

TDurden1937 (talk) 18:57, 28 September 2008 (UTC)TDurden1937


 * Creationists are the only people I have EVER seen use the lines "no extra information gets added" or "it's still within its same kind" (without ever defining "kind" of course), let alone in the same paragraph. To myself, Michael Johnson, and anybody else who's witnessed more than few creationism vs. evolution debates, it was immediately clear where Richard001 was trying to go with this. We've seen it a zillion times, and the lines are tiresomely predictable. You could almost turn it into a drinking game at this point.


 * More importantly, this page is NOT a place for having that kind of debate. If you really do want to get into that ever so tiresome debate about "adding new information" or "variation from a kind" that has already been done to death, then leave Wikipedia and go do a search on-line. Chances are you'll find at least 100 different forums where right at this very moment, some creationist is parroting the same exact arguments, under the stupid assumption that they've never been addressed.  WillieBlues (talk) 17:50, 28 August 2011 (UTC)

Am i involved in mutation?
My eyes were blue 'till i was 8, then they went blue/green then green then green gray to grey blue in the last 5 years, what kind of Mutation would that fall under??
 * I don't aactually know if this is mutation, but it is in fact very common for people's eyes to change colour, especially during puberty. I know mine went from blue to grey.-- Neo  Nerd  12:16, 26 June 2007 (UTC)
 * No, that is part of your own aging process. Mutations occur between generations. --Michael Johnson 12:26, 26 June 2007 (UTC)
 * Mutations occur in both sexual and asexual reproduction of cells. Mutations in sexual reproduction are more important because you start from only two gametes, and anything 'wrong' with them will be propagated throughout your body. In contrast, a mutation of a single cell will probably be unnoticeable, though it can still lead to problems, such as cancer. Your hair colour, eye colour etc changing is just normal maturation, part of the natural development process. Children often have blond or light coloured hair which gets darker as they grow up for example - mine used to be very blond. Richard001 02:55, 21 July 2007 (UTC)

Beneficial mutations ... or not?
This kind of follows on from the above Topic 'Mutations do not result in evolutionary change!', I came to this Article to find an example of a Beneficial Mutation, however the example that it provides is actually a deletion, according to the definition of Mutation, at the beginning of the Article, even a deletion is a Mutation! .... but isn't that then (Biological) Devolution? I mean, the example given is removing from the gene pool, it states "For example, a specific 32 base pair deletion in human CCR5 (CCR5-Δ32) confers HIV resistance..." what it is saying is that if you specifically remove or delete from CCR5 then the organism receives a benefit, this is subtraction not addition and therefore Devolution, not Evolution: The basic Dictionary definition of Evolution is "the way in which living things change and develop (in a beneficial way), Eg. moving from lower to higher life forms", Devolution is the opposite, "the way in which living things change and develop (in a harmful way), Eg. moving from higher to lower life forms", the Definition for Mutation at the beginning of this Article is too vague and broad. My understanding of Evolutionary Theory is that 'the 32 base pair in human CCR5' would have come about by Evolution in the first place ... therefore removing it is Devolution, this example is actually stating that the addition, through Evolution, of this 32 base pair in CCR5 was Harmful, therefore this example of a Beneficial Mutation is actually an example of a Harmful Mutation. Can (another) example of a Beneficial Mutation not be given? —Preceding unsigned comment added by Jon234567890 (talk • contribs) 11:25, 7 August 2007


 * Your comment appears to be trolling. I gave a perfectly good example in that above conversation. Perhaps something about the importance of duplication in the formation of beneficial mutations should be included in the article. Madeleine ✉ ✍ 14:23, 7 August 2007 (UTC)

Hi, thanks for replying, ... yes, your example was good, but it doesn't solve my problem, I came to the Article to get an example of a Beneficial Mutation, the Article's Example is actually a Deletion (biological Devolution) of Genes, Your Example was neither addition (Evolution) or subtraction (Devolution), your example however does perfectly show how duplication and rearranging already existing Genetic information can result in the biological advancement of a specie, called Evolution. The Article should, 1. Redefine it's definition of Evolution - or at least clarify it, and 2. The Article's Example of a Beneficial Mutation should be removed - or at least a comment made requesting an example to be provided for 'the Addition of genetic information, through a Beneficial Mutation', instead of subtraction, duplication, or rearrangement of already existing Genetic information. Jon234567890 15:30, 7 August 2007 (UTC)


 * Devolution has no meaning to a biologist. A deletion is a mutation. David D. (Talk) 17:33, 9 August 2007 (UTC)


 * It must be clear that evolution is not about adding, is about changing. There is no such thing as "devolution", removing unnecessary or nocive "information" is also benefical.  wildie  ·  wilđ di¢e  ·  wilł die  14:36, 10 August 2007 (UTC)


 * The example of the beneficial mutation is, in my opinion, a good one. But we should also add an example of a beneficial mutation in which information was added, not removed. Creationists often claim that evolution can't increase the amount of information and by only mentionning a beneficial mutation by deletion, we're not helping ourselves. Something about the fate of duplicated genes should be enough. - PhDP (talk) 18:54, 9 August 2007 (UTC)

From reading the Article & this page (and others on Evolution in Wiki), there appears to be four recognised forms of mutation, 1. The Duplication of already existing material (example given by Madeleine, above, about the "opsin in old world monkeys"), 2. The Deletion of already existing material (example given in Article), 3. The Rearrangement of already existing material, and 4. The appearance of New previously non existent material. We should list these four forms of mutation, AND list examples of each, with the exception of the third & fourth, for now, until someone can add good examples of them? Anyone, want to go ahead and amend the Article? --Jon234567890 09:46, 20 August 2007 (UTC)

Because deletion of even one allele for CCR5(Del32) is associated with an increased risk of West Nile Virus, and both deletions appear to be necessary to confer protection to HIV, I do not know that I would call it universally beneficial. A better example might be lactase persistance, which at least in some cases is an insertion (http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.37.110801.143820) and which so far has not been linked to any negative trade-offs (e.g. http://cebp.aacrjournals.org/cgi/content/full/16/5/956). Crummyusername (talk) 18:09, 19 May 2009 (UTC)Crummyusername
 * The common alleles for lactase persistence are usually base substitutions in the gene upstream of LCT. The assumption is that the substitution changes the regulation of the gene. David D. (Talk) 21:58, 19 May 2009 (UTC)
 * I just looked at the annual reviews you link to and they do refer to the common allele. It does not mention an insertion. I agree this is one of the least complicated examples of a beneficial mutation.  On the other hand, there should not be a misconception that positive selection only works on traits with no negative consequences.  David D. (Talk) 22:02, 19 May 2009 (UTC)

Beneficial, Harnful and Neutral mutations
It makes absolutely no sense to include Beneficial mutations and Harmful mutations in this article, but to have a separate article about Neutral mutations. Beneficial, Harmful and Neutral mutations should be included in a section on classification "By effect on fitness" (or something similar). - PhDP (talk) 20:01, 7 August 2007 (UTC)

Mutation is central to the theory of Evolution, specifically Beneficial Mutations; as Harmful Mutations will, through Natural Selection, be filtered out, and Neutral Mutations will have no effect. Therefore without Beneficial Mutation there can be no Evolution. To me it makes perfect sense to have the three types of Mutation (Harmful, Neutral & Beneficial) listed and explained because they are all forms of mutation, it then follows that it is good sense to list the process how these types of mutation occur, eg: deletion, duplication, etc. and then to list examples, such as evidence from research, etc. --Jon234567890 10:02, 20 August 2007 (UTC)

I have edited this section to point out that the fitness effect of mutations follows a continuous distribution. —Preceding unsigned comment added by 92.20.7.163 (talk) 10:46, 19 December 2009 (UTC)


 * Material added to Wikipedia should have a reliable source which shows it to be relevant. Simply adding statements, whether they are right or wrong, is pointless unless you can back them. Even if the distribution is continuous, is it skewed? Can you show the that the cutoffs on either side of neutral are wrong? As the fitness effect of some mutations may be deleterious, except in specific conditions (e.g. sickle cell in malaria-rich regions), this is difficult to quantify, but population equilibria offer a test. The nearly neutral theory of molecular evolution offers a model where drift vs. selection can be assessed. An unsupported blanket statement is of no use. (And please remember to sign your posts with four tildes— "~" .) Novangelis (talk) 15:31, 19 December 2009 (UTC)

The Distribution of Fitness Effects of nonsynonomous mutations is inferred from the Site Frequency Distribution (i.e. the allele frequncy distribution). For example, if most mutations are present at a low frequncy, this is evidence of the presence of slightly deleterious mutations, as negative selection will attempt to drive the frequency of deleterious mutations down. If mutations appear at a mixture of low, through intermidate to high frequencies, then this is evidence of the presence of advatageous mutations, as these mutations will generally reach a higher frequency in the population due to positive selection. What exactly this distribution look like (e.g. to what extent may it be skewed towards deleterious mutations) is still an active area of research, and appears to vary between species. See this review paper, for an overview of the Distribution of Fitness Effects: http://www.lifesci.susx.ac.uk/home/Adam_Eyre-Walker/Website/Publications_files/EWNRG07.pdf I don't know how to sign off, but here goes an attempt. Regards, Chris92.20.7.163 (talk) 10:56, 20 December 2009 (UTC)

The transmission of somatic mutations in animals

 * In multicellular organisms, mutations can be subdivided into germ line mutations, which can be passed on to descendants, and somatic mutations, which cannot be transmitted to descendants in animals. 

I think a whole lot of animals that reproduce via fragmentation can in fact transmit somatic mutations. It wouldn't be the "animalness" versus "plantness" of an organism that determines the viability of transmission of somatic mutations, but rather the degree of organ specialization for reproductive function, and how much it can "filter" somatic mutations. But even then, if the tissues responsible by gametogenesis themselves had somatic mutations, or even some of their cells, I think that they would produce gametes with the inherited somatic mutation, anyway. But I don't know if the latter would count as somatic mutation. --Extremophile 19:41, 2 November 2007 (UTC)

Chromosome 2
I came to this article to see if I could add (or learn) anything regarding chromosome 2, but I'm now slightly confused. Neither the illustration or the article seem to address the fusion of two distinct chromosomes that led to the creation of the single chromosome 2. What am I missing? Tomandlu 13:05, 14 November 2007 (UTC)
 * You shouldn't be looking for information about specific mutations on this page. See instead Robertsonian fusion and Chromosome 2.
 * There is case for mentioning monosomy, trisomy, chromosomal fusion and fission, and polyploidy among the categories of mutation, but there's no pressing reason why the origin of human chromosome 2 should be mentioned in this article. Lavateraguy 16:00, 14 November 2007 (UTC)


 * Sorry, I should have been clearer - it was the lack of reference to fusion and fission amongst the type of mutations (and the illustration) that confused me (not the lack of reference to chromosome 2). Are fusion and fission sub-types of any of the mutations referred to, or something else? Tomandlu 16:40, 14 November 2007 (UTC)
 * Fusion (Robertsonian fusion/translocation) seems to be a form of translocation. I don't know how fission works (generalising from those plants with diffuse centromeres may not be valid), so I can't say whether it is a subset of any other type.
 * I've added some See Also entries as a temporary band aid. —Preceding unsigned comment added by Lavateraguy (talk • contribs) 17:15, 14 November 2007 (UTC)

How common?
This article doesn't say how common mutation is. I think this would be a very beneficial addition to the article, especially the human mutation rate. I've seen figures from 0.7 to 100 mutations per person. Can anybody come up with a reliable reference? Herorev (talk) 03:42, 27 December 2007 (UTC)


 * Mutation rate varies extremely. Additionally, human mutation is the smallest example of organic mutations, so mentioning this sort of hypothesis/data would be getting too biased for comfort.

Lethal
User:TimVickers asked 'Why would lethaility be beneficial to an organism? Discuss on talk page please'; i'm certainly no expert, but my understanding is that some mutations that lethal when reinforced are beneficial when on a single chromosome. The one that springs to mind is that for sickle cell anæmia, which provides some resistence to malaria when not reinforced. Does that help? Cheers, Lindsay 12:10, 26 March 2008 (UTC)
 * It seems to me that it is more likely that the second occurrence of lethal in the reverted text was an error. Anyway, the reverted text was redundant. Lavateraguy (talk) 12:46, 26 March 2008 (UTC)

The nature of the genotype is the real issue here. A fully dominant or fully recessive lethal is unlikely to be beneficial to an organism. The key with sickle cell anemia is that it is partially dominant (codominance or Incomplete dominance are typical). David D. (Talk) 15:54, 26 March 2008 (UTC)

Do spontaneous mutations only occur before birth?
Or can they also occur during an organisms lifetime? —Preceding unsigned comment added by 72.65.178.6 (talk) 19:43, 1 April 2008 (UTC)


 * Mutations will occur at all points in an organism's lifetime. Tim Vickers (talk) 20:32, 1 April 2008 (UTC)

I know induced mutations happen throughout an organism's lifetime, but don't spontaneous mutations only occur during DNA replication or no? —Preceding unsigned comment added by 72.65.178.6 (talk) 04:58, 2 April 2008 (UTC)


 * Spontaneous mutations can occur at any point in the cell cycle and cells never stop dividing throughout the lifetime of an organism. The bodies of organisms are being constantly renewed. Tim Vickers (talk) 15:38, 2 April 2008 (UTC)

Why is amino acid residue hydropathy and molar volume encoded in the genetic code prior to translation?
Doug Youvan (talk) 04:10, 24 April 2008 (UTC)

I'm sorry I don't understand either the question or the relevance of the topic to mutation. Could you rephrase your comment? Tim Vickers (talk) 02:42, 25 April 2008 (UTC)


 * The source of the figure is here: http://www.complexity.org.au/ci/vol01/fullen01/html/ and that on-line paper's references will show a few interesting things: 1) the structure of a membrane protein can be predicted from the nucleotide sequence (without translation), because the correlation between the structure of the genetic code and the the hydropathy of the amino acids residues is significant, 2) Singular Value Decomposition (SVD) can be used to map amino acid residue hydropathy and molar volume (separately) back onto the triplet codon as a function of the position in the codon and the nucleotide used, and 3) the genetic code as it stands is special as compared to random codes for supporting in vitro directed evolution experiments wherein genetic algorithms (theory and practice) are used to guide the 'doping' of codons in synthetic DNA for combinatorial mutagenesis.


 * So, my question can be rephrased as follows: Why is the genetic code structured in a manner that predicts (another word might be better ?) the two most important properties of the amino acid residues?  I don't believe there is a known feedback mechanism to select for a particular code, nor is the subject discussed much.  It would seem that a hypothetical evolutionary selection on the primordial code might have lead to several different codes which we do not see.  Any references to this that we can cite? Doug Youvan (talk) 03:14, 25 April 2008 (UTC)


 * I should add that there is a related discussion here Talk:Moore-Penrose_pseudoinverse where readers of this discussion should recognize "alphabet = 4" as the four nucleotides, and "word = 3" as the triplet (3) codon. Using that math, the conventional PsuedoInverse (from SVD) is not needed for matrices structured such as the genetic code.  It's unclear whether that is a special and / or trivial solution to P = NP. Proper referencing to encyclopedic quality work is needed in that case, too. Doug Youvan (talk) 03:32, 25 April 2008 (UTC)

Suppressors and Enhancers
Shouldn't we add Suppressors and Enhancers as types of mutations? --Kupirijo (talk) 22:26, 2 June 2008 (UTC)


 * Are you referring to regulatory elements of the genome? You could have mutations in a promoter region, but they are the same kinds of mutation that have already been described in this article (although the affects may be more noticeable, given that these regions are not transcribed and the redundancy of certain bases as a result of codon translation therefore does not exist here) Ethidium (talk) 07:58, 25 July 2008 (UTC)
 * This is a case where the study of usage would not go amiss, but mutations, not necessarily in regulatory elements of the genome, can suppress or enhance the phenotypic effect of other mutations. Lavateraguy (talk) 08:49, 25 July 2008 (UTC)

"mutant" picture
The picture of the dog that is displayed near the bottom of this page probably isn't the result of a mutation. It's much more likely to be a developmental abnormality caused by incomplete cleavage of the developing embryo. Unless there is some evidence supporting a genetic cause for the abnormality, it would be better to leave it out, as it supports the vernacular understanding of the term. I think some forms of albinism are the result of mutations, and would provide a less ambiguous example.

Additionally, an example of a mutation that can be beneficial is the beta-globin point mutation that causes sickle cell anaemia, which although debilitating in most cases, also provides some resistance to malaria. —Preceding unsigned comment added by Ethidium (talk • contribs) 13:50, 24 July 2008 (UTC)


 * I agree with this anonymous editor. In fact, I thought we had removed this picture already. Anyone have any history/opinions? Tan      39  13:53, 24 July 2008 (UTC)


 * In fact, it might even be worth keeping the image to explain why it is NOT a mutant (alongside an image of an actual mutant) Ethidium (talk) 14:01, 24 July 2008 (UTC)


 * I reverted the image when it was first introduced, on the grounds that it was a conjoined twin, and not a mutation. The original editor put it back, claiming that it wasn't a conjoined twin. Lavateraguy (talk) 14:41, 24 July 2008 (UTC)
 * Well, as it is now, it's pretty much false information. I say we remove it for now; if someone wants to do the "comparison" composite as Ethidium suggested above, it can be added later. Tan      39  14:43, 24 July 2008 (UTC)
 * I removed the dog image. It is very likely not a mutation but a developmental abnormality.  There are better examples out there.  If someone can verify the providence of the picture and a scientific explanation for it then it can be added in.  The caption under it should then describe the mutation causing the disorder.  Conjoined twins in a jar do little service to the subject of the article.Capeo (talk) 20:11, 9 September 2008 (UTC)

Types of mutation vs. Classification
Is the "types of mutation" section really not just a classification by impact? It probably should be brought down a level. Novangelis (talk) 00:47, 21 November 2008 (UTC)

Protection
Could somebody protect this article? Because almost all of the last 20 or so editions were vandalism... --3M (talk) 00:25, 10 January 2009 (UTC)

define these
cystic fibrosis and genetic disorder —Preceding unsigned comment added by Sajidsa13 (talk • contribs) 17:28, 11 March 2009 (UTC)

We're not here to do your homework. Check cystic fibrosis and genetic disorder. Murphy2010 (talk) 20:20, 1 April 2009 (UTC)

Removed paragraph
I just removed the following paragraph from the "Benefical mutations" section. It's clearly not about beneficial mutations but if someone wants retrieve something useful from it here it is:

Long before the advent of genetic testing or even complete understanding of DNA and RNA, astute observers noticed that genetic traits, including many disorders, were passed from one generation to another in somewhat predictable patterns. These came to be known as autosomal dominant, autosomal recessive, X-linked recessive and X-linked dominant patterns of inheritance.

Chromosomes come in pairs in the cell's nucleus. Humans have 46 chromosomes in each cell nucleus, which are actually 23 pairs of chromosomes. For 22 of these pairs, numbered chromosome 1 through chromosome 22, the chromosomes are the same; that is, they carry genes for the same traits. One chromosome comes from a person's mother, the other from his father. The 23rd pair is an exception and determines gender. The 23rd chromosomal pair differs according to whether you're a male or a female. Males have an X and a Y chromosome, while females have two Xs for this 23rd pair of chromosomes.

U.S. scientists have found a single change in the DNA of mitochondria -- enzymes that generate energy in human cells -- can cause heart and muscle disease.

-- §hanel  09:18, 7 April 2009 (UTC)

Genetic Disorder?
What's the difference between a "genetic disorder" and a mutation? According to what I read, things like Marfan's Syndrome and Down's Syndrome are labeled genetic disorders. Are they in fact recurrent mutations or something else? Virgil H. Soule (talk) 04:02, 9 July 2009 (UTC)


 * A mutation is simply the actual, physical change in the DNA. Mutations occur for a number of reasons, most usually radiation, chemicals, or random chance, and can be deleterious, beneficial, or completely silent with no change whatsoever.  Genetic disorder is something (negative) caused by some kind of funkiness in the genetic code.  Some genetic disorders can be a result of mutation, such as Sickle-cell anemia, but they don't have to be.  Down's, for example, is caused by a third copy of the 21st chromosome - that's not really a mutation, but rather an error in genetics, a disorder.  Marfan's, AFAICT, is caused simply through genetics.  You can call it a persistent mutation, but at a certain point it's just a gene or allele - kidneys are persistent mutations. ~ Amory ( user  •  talk  •  contribs ) 05:20, 9 July 2009 (UTC)


 * The article gives the impression that mutations are spontaneous aberrations in gene structure resulting, say, from random copy errors. Do we know why some "mutations" recur, e.g., Down's? I saw a program about Primordial Dwarfism on TV. This one couple had a child diagnosed with the syndrome. They were assured by experts that the malady was a 1-in-a-million accident and wouldn't happen again. So, they had another child and, lo and behold, that child also was diagnosed with primordial dwarfism. Evidently, both parents were "carriers" of an aberrant allele that was expressed as primordial dwarfism in their children. Which brings me back to my original question: Do mutations actually occur or is the human gene pool carrying along a large number of aberrant alleles that appear as genetic disorders in our children? With reference to the article, is the term, mutation, over-used or perhaps even mis-used? --Virgil H. Soule (talk) 19:51, 6 August 2009 (UTC)


 * Some mutations are more common than others for different reasons, depending on the mutation. With Down's, it's a chromosomal abnormality that happens to not be lethal, you don't see trisomy 3 because that chromosome is so large that the wrong number outright kills the developing embryo. (Chromosomes are numbered in descending size based on their visual appearance when discovered, btw, roughly correlates with DNA length.) The case you're talking about appears to be one where the doctors assumed a spontaneous dominant mutation was responsible (as is the case with achondroplasia (possibly misdiagnosed the child) but it turned out to have a different genetic basis caused by recessive versions, in which case 1/4 children has a chance of getting it.
 * There is a general theme that might help you understand: to simplify, there's two types of effects a version of a gene can have, "dominant" (just one copy causes something to happen) and "recessive" (both copies have to be there). It's like a dominant gene is actively bad and a recessive one is passively bad. (Dominant genes might even be so bad that having two copies is lethal.) Spontaneous mutations often give rise to people with diseases caused by dominant genes, these genes can't hide - examples are Marfan's syndrome and achrondroplasia. Recessive mutations are the ones where, if you get an unlucky combination of parents where each has one recessive, each child has a 1/4 chance of getting bad versions from both parents - *not* a spontaneous mutation - examples are cystic fibrosis and sickle cell anemia. Both mutations and aberrant alleles are occurring, it depends on the disease which one is typical. Madeleine ✉ ✍ 00:16, 3 September 2009 (UTC)


 * It seems to me that the term "mutations" was being misused to mean genes that varied from the modal average.(87.80.103.44 (talk) 18:34, 28 January 2010 (UTC))


 * I don't think anyone has ever got sickle cell anaemia by mutating.(87.80.103.44 (talk) 18:34, 28 January 2010 (UTC))


 * The only reason there is any variation in genes is due to mutation. Every allele that we see, whether it results in a normal phenotype or one regarded as a disease, came about originally by mutation.  The frequency of de novo mutation to the sickle-cell allele is low, but it undoubtedly occurs occasionally, and of course it has to have occurred sometime in the past to give rise to the sickle-cell alleles we now see.  Agathman (talk) 18:42, 28 January 2010 (UTC)

Mutation Rate
The article says nothing about mutation rate. which in humans, is about 150 per person or generation. Do these mutations accumulate over several generations or are they just genetic "noise" producing variations in hair color or the length of one's fingers? If they're cumulative, why do we look like Cro-Magnons who lived 30,000 years ago? --Virgil H. Soule (talk) 23:51, 2 September 2009 (UTC)


 * The article on mutation rate has that number, though.
 * The number I believe you meant was 150 bases of DNA per generation. There are 6 billion bases of material in each person's genome, though. Assuming an average generation time of 10 years, in 30,000 years that's only time for 450,000 bases to have changed, or .0075% of the genome. Maybe 150 bp/generation is far too low a guess; the article notes that guesses have varied by orders of magnitude, so we may just have to wait for whole genome sequencing to nail this down. Also, note that most of these changes are occurring in places where they have no effect; the protein coding regions of the genome is just ~1-2% of the whole genome, most of it is "junk DNA" filled with accumulated and suppressed parasitic elements.Madeleine ✉ ✍ 00:23, 3 September 2009 (UTC)

Antibody Hypermutation
The article doesn't seem to cover the intentional fast mutation of the variable regions of antibodies, which is the basis of the immune response, as far as I understand. This is a very important function of mutations, which is very different from the normal mutation function. I think the article should cover it. —Preceding unsigned comment added by 79.181.18.155 (talk) 02:01, 5 September 2009 (UTC)


 * Please take a look at Mutation under 'induced mutations.' (216.128.93.23 (talk) 23:59, 7 October 2009 (UTC))

Neutral vs. Detrimental
A user keeps changing "most mutations are neutral" to "most mutations are deleterious". I'm pretty sure the former is correct, but I'm not a biologist. What's the scientific consensus on this? thx1138 (talk) 22:59, 10 November 2009 (UTC)


 * If a mutation changes the amino acid sequence of a gene product, it will usually be detrimental if it is in a gene but doesn't change the aa sequence of the product, or if it is not in a gene, it is usually neutral . Tim Vickers (talk) 23:28, 10 November 2009 (UTC)

The name for the part of a gene sequence where it is different from the gene sequence it has been altered from
I don't know the name for this. Does anyone think it is "mutation". I have tried to reduce to ambiguity in the definition of "mutation" at the begining of the article by modifying it but I am not sure that I have got the definition quite right as yet. (87.80.103.44 (talk) 16:15, 28 January 2010 (UTC))


 * I'm not quite sure if this is what you're asking, but a mutation is a change in the DNA sequence (whether in a gene or not). The same term is also used for that altered sequence itself, so "mutation" can refer to the event -- sequence changing -- as well as to the product -- changed sequence.   The definition at the beginning is concise and correct; I'd leave it alone.  Agathman (talk) 16:57, 28 January 2010 (UTC)


 * A site that is different between two genes is also called a single-nucleotide polymorphism (if small) or an indel if larger. Hope this helps. Tim Vickers (talk) 17:05, 28 January 2010 (UTC)


 * Well, 87.80.103.44 just reinstated the change that I already reverted once. I'm not going to revert again, but as I explained above, mutation is not only the process that causes changes; it's also properly the term for the change itself.  I prefer the original wording. Agathman (talk) 18:19, 28 January 2010 (UTC)


 * My Oxford Dictionary of Biochemistry and Molecular Biology gives three meanings for the word "mutation", it firstly defines a mutation as "the process by which genetic material undergoes a detectable and heritable structural change", secondly as "any modified gene arising from a mutation" and thirdly as "a mutant". Tim Vickers (talk) 18:31, 28 January 2010 (UTC)