Talk:Mutation

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[edit] 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)

[edit] 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)

[edit] 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.

[edit] 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)

[edit] 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 [1]. 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.
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 [2]. 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 [3]. 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)

[edit] 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)

[edit] 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)

[edit] 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)

[edit] 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

[edit] 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)

[edit] 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 Wikipedia:External_peer_review/Nature_December_2005/Errors#Mutation. - 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)

[edit] 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)

[edit] 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)

[edit] 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?

[edit] 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)

[edit] evowiki unreachable

nslookup evowiki.org

      • rns00.ka.rz-ip.net can't find evowiki.org: Non-existent host/domain

same for www.

      • 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.

[edit] 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)

[edit] 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)

[edit] 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)
'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)
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