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Talk:Phylogenetics

Possible stolen images
It appears that the pictures in the Phylogenetic Tree Shapes section are stolen from another site. Omitting these, and possibly the whole section, might be good for the article. — Preceding unsigned comment added by LSpeakmanOU (talk • contribs) 02:25, 4 July 2024 (UTC)

from VfD
On 28 Mar 2005, this article was nominated for deletion. See Votes for deletion/Phylogenetics

The Picture
The picture on this article is technically a cladogram, not a phylogeny. This is because it does not incorporate environmental or temporal information. —The preceding unsigned comment was added by 12.217.236.33 (talk) 23:04, 18 February 2007 (UTC).

There is an understood temporal component in all cladograms. The deeper branches are older. The term phylogeny is appropriate here as well as cladogram.

I should like to attract attention to the colouring of the diagram: what does the connection in red between the birds (where is actually turns orange: why is the overlay area between blue and yellow not green????????) and the mammalians stand for? There is no common ancestor to these branches who was warm blooded and we have an independant evolution of this feature: so what does this connection try to suggest here? Or does it simply attempt to confuse and render incomprehensible what is essentially straightforward??? —Preceding unsigned comment added by 80.132.203.205 (talk) 13:23, 6 February 2008 (UTC)

 * Oh dear, oh dear... How are we ever to get out of Hennig's confusion (i.e., cladism)? A phylogenetic tree illustrates a 4D reality in 2D, thus by necessity confusing two dimensions, namely time and space. A phylogenetic tree traditionally conveyed information about either relationship or properties (the two phenomena that was confused in the dimensional reduction), consistently joined in a conceptualization of the Linnean kind (i.e., categories of categories). Now, Hennig's comprehension boldly confused the 4D reality with the 2D illustration thus introducing a new kind of dichotomous illustration that he (or his successors) called a 'cladogram'. This kind of illustration, or rather this kind of interpretation of this kind of illustration is thus a conceptual confusion confusing the concepts time and space.

 * The picture on this article is thus not "technically a cladogram, not a phylogeny". It is an illustration of the relationship between the terminal units. However, its definitions of poly-, mono- and paraphyletic groups is biased towards cladistics by deeming paraphyletic groups to be non-monophyletic and excluding holophyletic groups (see Envall ). The problem with its partitioning of reality into these different kinds of groups is that it it based on this 2D-illustration of a 4D phylogeny. It does in practice not partition reality into different kinds of things, but instead classifies this dimensional reduction into different kinds of things. It classifies a classification. The problem with it is thus not what it is, but what it is interpreted as. Including the partitioning into kinds of groups, it is not an illustration of phylogenetics, but of cladistics. It is thus an erroneous confusion of the concept 'cladistics' with the concept 'phylogenetics'. These two concepts are not equal or even synonymous. The former (i.e., cladistics) is actually a specific kind of conceptualization of phylogenies, which Envall explains is inconsistent, self-contradictory and (empirically) wrong. —Preceding unsigned comment added by 83.254.20.53 (talk) 23:08, 21 September 2008 (UTC)

Phenetics and cladistics as methods
The article's statement that "The most commonly used methods to infer phylogenies include cladistics, phenetics, maximum likelihood, and MCMC-based Bayesian inference." is a bit puzzling. (This is part of what I think is a general muddle over the term "cladistics"). The declaration that one method for inferring phylogenies is "phenetics" is strange, since phenetics as a philosophy of classification is positively uninterested in phylogenies and interprets its branching diagrams as classifications but not as phylogenies. What is going on here is to label parsimony methods "cladistics" and distance matrix methods "phenetics". In my view these latter two terms are best reserved as labels for approaches to classification, not methods for inferring phylogenies. The two get middled together all the time. (But keep in mind that in systematics this view of mine is considered by most people as dubious and marginal -- when it comes to this view I'm regarded as a fringe crackpot.) Felsenst
 * I made these changes to the wording of that section. It's a drop in the bucket compared to what's needed with this article.  --Aranae 17:15, 5 July 2006 (UTC)

 * User Felsenst is correct. Neither cladistics nor phenetics are "methods to infer phylogenies". This statement is instead a symptom of the cladistic confusion. I am a personal friend to Swofford, and I can assure Felsenst and everyone else that neither Felsenstein not Swofford would ever accept this confusion. The problem is Hennig's confusion of reality and our illustration of it. I am prepared to write a comprehensive explanation of what phylogenetics is, but since I explain that cladistics is inconsistent, self-contradictory and wrong, I constantly get deleted and blocked. A consistent explanation of phylogenetics will show cladistics to be wrong, and cladists therefore delete and block phylogeneticists (like me). Consist (presently at 83.254.20.53 (talk) 23:21, 21 September 2008 (UTC)).

embryology
would sympathtic editors consider a positive vote here? Slrubenstein  |  Talk 15:18, 23 August 2006 (UTC)

Monophyly, paraphyly and polyphyly merge
(Moved to talk:clade). Richard001 06:58, 4 November 2007 (UTC)

 * See the explanation of the concepts in Envall —Preceding unsigned comment added by 83.254.20.53 (talk) 23:23, 21 September 2008 (UTC)

Lumping and splitting
Would a discussion of "lumping" and "splitting"—what the terms mean, and how authorities come to such decisions—be warranted here? MeegsC | Talk 15:40, 20 May 2007 (UTC)
 * At present this article is rather short, and such a new item might be out of proportion. But do take a look at Lumpers and splitters. The topic is explored there in some depth. EdJohnston 16:15, 20 May 2007 (UTC)

 * "Lumping and splitting" in biological systematics is actually extremely interesting on the most fundamental (generic) level, and therefore should not be discussed in this article. Basically, it concerns the fact that reality can be comprehended in terms of yes's and no's, which cannot sum up to one (exactly the opposite to what the probability for each does). This fact occurs in statistics in the form of Type 1 and Type 2 errors, that is, falsifying a true hypothesis respectively accepting an erroneous hypothesis, and in cartography by the different aspects on accuracy, that is, the probability that a randomly chosen position on the map is correctly classified respectively the probability that a randomly chosen position in reality is correctly classified. In the case of "lumpers and splitters" in biological systematics, this fact means that partitioning reality according to similarities or differences simply cannot give the same result. Getting the same result is just as impossible as that Type 1 and Type 2 errors is the same; if they had been, they wouldn't have been different. At the most fundamental level, it is the fact of the impossibility that a difference can be a similarity.

 * Now, cladists think that this fact is just a consequence of conceptualization itself, thus claiming that a confusion of conceptualization is "natural", but it is wrong. This fact actually has roots in reality, as witnessed by the fact that time is relative. It suggests that this fact is the reason for process itself by meaning that reality simply cannot find a stable configuration per definition. Whatever the reason for the fact is, it means that our conceptualization of reality in terms of generics and specifics is a consistent handling of this fundamental fact. Cladists are thus totally wrong. They obviously do not recognize this fact, much less understand the complicated relation between concepts and reality. They actually appear to be totally ignorant of everything that preceded, or exist in parallell, to cladism. They are true extremists: don't discuss anything in other terms or conceptual frameworks than you self decide. In the light of cladism, "lumpers and splitters" do not even exist. They are burried in its coding of characters and character states. The fundamental ambiguity is swept under the mat pretending that it does not exist. I am this fact trying to get out from under the mat, and they, led by Sjö, constantly pushes me back under the mat.

 * After this comment, I will probably be blocked till at least the 10th of December, and probably by Sjö. I will, however, be back either when the blocked is lifted or under another ip-adress. Typical for cladists is that they think that things have a mandatory connection to their addresses (i.e., properties), and thus cannot escape them. I will show them that they are wrong. —Preceding unsigned comment added by 83.254.20.59 (talk) 01:15, 7 November 2008 (UTC)

Cladistics a synonym for phylogenetics?
Ernst Mayr would be rolling in his grave. I think this should be reverted. Cladistics is the Hennig school, and their view of how things go in phylogeny is far from universally shared. One of the problems is that the different authors give their own meanings to the words, and then assume that those meanings are universal. Phylogeny comes from the 18th century, before cladistics was thought of. All we should do is cover the controversy, without picking winners and losers. EdJohnston 19:43, 14 November 2007 (UTC)

Phylogenetic Systematics and Cladistics are two different approaches to interpretations of evolutionary relationships. They should not be used synonymously as phylogentic systematics takes in consideration of ALL homologous characters, whereas cladistics considers specifically chosen derived characters to reach generalizations of evolutionary relationships. This process results in a development of a phylogenetic chart showing relationships through time with hypothesized ancestor-descendant links (phylogenetic systematics) or a cladogram with no ancestor-descendant links hypothesis AND without a time dimension. Timothy Michael Earwood 04:40, 27 January 2008 (UTC) —Preceding unsigned comment added by Poethical (talk • contribs)

 * EdJohnston is right, not because "Ernst Mayr would be rolling in his grave", he was pretty incomprehensible himself, but because phylogenetics is not a synonym to cladistics. Phylogenetics denotes a science that discusses dichotomously branching processes, whereas cladistics denotes a confusion of reality and our illustration of it concerning dichotomously branching processes. Phylogenetics is thus the science, whereas cladistics is an inconsistent, self-contradictory and (empirically) erroneous comprehension of phylogenies. —Preceding unsigned comment added by 83.254.20.53 (talk) 23:38, 21 September 2008 (UTC)

Who is this Williamson?
"Williamson believes that larvae and embryos represent adults in other taxa that have been transferred by hybridization (the larval transfer theory)"Who is Williamson, why is he important, why should we care about his ideas, what exactly are his ideas anyway and what does hybridization or larval transfer mean in this context? Some of the readers are not as familiar in the field of developmental biology as you are, please try to keep that in mind. Shinobu 12:57, 4 December 2007 (UTC)

I have no idea why this passage about Williamson is included. At best, it is a wild conjecture that is far outside of mainstream evolutionary biology! — Preceding unsigned comment added by 141.217.188.92 (talk) 21:17, 17 October 2011 (UTC)

The "Williamson" mentioned is this guy. Saying his views are a wild conjecture is a great understatement -- they are totally off the wall. See the "Controversy" section of that Wikipedia page. Felsenst (talk) 21:47, 30 November 2011 (UTC)

Cladistics is a method to do ... what?
The article currently says: Cladistics provides a simplified method of understanding phylogenetic trees. ....

The most commonly used methods to infer phylogenies include parsimony, maximum likelihood, and MCMC-based Bayesian inference. Distance-based methods construct trees based on overall similarity which is often assumed to approximate phylogenetic relationships. So is "cladistics" a method of "understanding" trees, or constructing them? Are parsimony, ML, and Bayesian methods examples of "cladistics"? Or not? Or do they reconstruct the trees which are then "understood" by cladistics? Also, why are distance methods "assumed to approximate phylogenetic relationships" but likelihood and Bayesian methods, which are based on the same models, not making that assumption? (Don't mind me, I am just harassing folks in this field because I think the standard descriptions of what is going on are totally muddled, and this article reflects that). Felsenst (talk) 20:28, 19 March 2008 (UTC)
 * Hello, Professor F! We do have an article on Cladistics, but I believe it is an imaginative reconstruction of what the field ought to be, not referenced to reliable sources. (The content of Wikipedia articles may ironically reflect the popular understanding of certain topics, even when it diverges from the sources). I have a sense that it would be easier to reform our article on Maximum parsimony if anyone had the patience to begin. There is probably a real story to be told there, for which strong references could be found. Since that article at present has no inline citations, the rationale for re-writing is evident. EdJohnston (talk) 21:03, 19 March 2008 (UTC)

 * The article is written by a cladist. I (Envall ) have explained that cladism is inconsistent, self-contradictory and (empirically) wrong. Cladism is actually the ultimate conceptual confusion, confusing all concepts. I claim that Wikipedia have to discard cladists to make an encyclopedia. Cladists do not distinguish concepts, but confuse concepts. Allowing them to influence Wikipedia is like letting the fox into the hen-house. Cladists are confused. They are actually paranoic. They ought to be in treatment rather than in scientific discussions. Consist (presently at 83.254.20.53 (talk) 23:48, 21 September 2008 (UTC))

 * Wikipedias' problem is just to shut off believers from being administrators. Belief does not agree with knowledge per definition. Wish cannot be combined with skepticism.
 * An encyclopedia has to rest on skepticism to fulfill its aims. Distinguishing belief from skepticism is the grand problem for Wikipedia's administrators. If they succeed, Wikipedia will be a good encyklopedia, but of they fail, Wikipedia will split into several encyclopedias. Consist, presently at 83.254.20.59 (talk) 00:38, 8 November 2008 (UTC)

Obsolete sentence
The intro contains the sentence "The problem posed by phylogenetics is that genetic data are only available for the present", and cites a 1967 journal, but this is no longer true. DNA sequencing has been performed on ancient organisms, including mammoths frozen in permafrost, and insects embedded in amber. This is not my field and I don't have readily available references, so please accept this request for an update. --Blainster (talk) 16:02, 4 July 2008 (UTC)

Is this article about phylogenetics or cladistics?
When reading the page, I get confused by the constant inflictions of references to cladism. Why is the same picture included in this article as in the article about cladistics? Envall has recently shown in Biol J Linn Soc that cladistics actually denies both facts and science, why should it be allowed to confuse itself with the science of phylogenetics? Can't it stick to its own article (where it, by the way, refuses to include criticism of it). Is cladism allowed to infect all articles discussing evolution? Consist (talk) 23:32, 8 July 2008 (UTC)

Am I allowed to change this article
Am I allowed to change this article without being deleted or blocked? Consist (presently at 83.254.20.53 (talk) 23:53, 21 September 2008 (UTC))

 * Anyone can make constructive contributions. If they are made in good faith and constructive but wrong they may be deleted, but you won't be blocked unless they are clearly vandalism or construed as such. Plantsurfer (talk) 07:54, 22 September 2008 (UTC)

 * No, not in this case since user:Consist is permanently blocked for pushing his own research.Sjö (talk) 15:10, 23 September 2008 (UTC)

Phylogenetic systematics or cladism?
How come an explanation of the concept phylogenetics in the beginning contains the expression "phylogentic systematics or cladism", thus equalizing the two? What on earth does a science has to do with an extremism of that science? Phylogenetics does not require acknowledgement of the inconsistent, self-contradictory, empirically erroneous and ambiguous concept "clades". This acknowledgement is actually a bold confusion of process and pattern, that is, only an extremism kind of phylogenetics. Is islam equal to alQuiada? Consist, presently at 83.254.20.122 (talk) 00:19, 6 November 2008 (UTC)
 * First of all, might I suggest you calm down a bit? You analogies are bad and you come across confrontational. Always assume good faith. There are plenty of references where "phylogenetic systematics" and "cladistics" are referred to very nearly synonymously (see the references at the end of the Cladistics article). Note that it is "phylogenetic systematics" and not "phylogentics"; there is a difference. I am not sure where you find clades to be "self-contradictory" or "empirically erroneous". Obviously, it is a changing science. We are constantly revising the Tree of Life. However, if you can prove something to be wrong, feel free to add it to the article. It is easy to throw around claims and criticisms, but you must back them up (and not with your own research, as I suspect is the case). --Thorwald (talk) 19:37, 6 November 2008 (UTC)

 * I am calm. My analogy focuses on the fact that both are confusions of a generic with one of its specifics. The fact that there are many people in biological systematics that presently make this confusion doesn't mean that it isn't a confusion. Thorwald also appears to understand that it is a confusion, as judged by his expression "very nearly synonymously". It actually means not synonymous, because a close hit is not a hit. Cladistics does, of course, rest on the concept clades, and Envall has explained exactly how this concept is inconsistent (i.e., self-contradictory) and empirically erronous. It does, however, not mean that phylogenetics, or even phylogenetic systematics is afflicted with these errors. The errors resides solely in the distinction of clades, manifested in the "denial" of paraphyletic groups. The truth is that "clades" ought to be called holophyletic groups (as also Ashlock explained long ago), and that both holo- and paraphyletic groups are monophyletic groups. Cladism "sinks" (or drags) holophyletic groups into monophyletic groups thus making them "very nearly synonymous". To really nail their synonymonity (is that correctly spelled?), it actually defines that they are synonymous, thus inconsistently (meaning self-contradictory) and empirically erroneously. They are not, I repeat not, nor can be, synonymous. I beg the administrators of Wikipedia to pull this confusion apart. Cladism can't be made synonymous to phylogenetics (or phylogenetic systematics) by any definition(s) in the universe. They are as different as fruits and pears are. Cladism is actually applied conceptual confusion. Let it play in its own sandbox. Its inherent inconsistency means that it will split into thousands of pieces as time passes. It is the donkey's chase for the carrot in front of his eyes and thus, incidently, also golden pants in science. Does anyone see the problem? Consist, presently at 83.254.20.59 (talk) 00:15, 7 November 2008 (UTC)

 * I apologise. I misunderstood what you were arguing (originally). I understand now and very much agree that there is a common confusion, even among those doing phylogenetics. And, yes, that is why I wrote "very nearly synonymous". I didn't know how much the reader would understand the concepts of holo-, para-, and mono-phyletic. This comes up very often when I TA a class for students learning MrBayes. As we are always looking for the "optimal" tree, the students constantly think of clades. We really should switch to using mono- and para-phyletic when ever someone tries to use "clade". Note that you don't need to be an administrator of Wikipedia to help re-write this article and present it more as it would appear in the field (but, of course, always remembering that a layperson might be reading it). Thanks for taking the time to explain. I suppose I should have taken more time to read your original post. --Thorwald (talk) 01:36, 7 November 2008 (UTC)

 * Finally reaching common ground. However, when you wrote that "We really should switch to using mono- and para-phyletic when ever someone tries to use "clade", I suppose you mean holo- and paraphyletic groups. My original reason for pursuing this battle against cladism is that it unlegitimately "denies" reconstruction of phylogenetic units "from the inside and out", that is, in terms of less inclusive units forming more inclusive units (for example populations forming species), although it has developed into an existential matter, that is, a matter about facts. I have gradually reached a deeper understanding of the problem and have thereby understood that it is actually very simple, although very difficult to understand.

 * The simple explanation is on an existential level that "pattern isn't process", and on a conceptual level that "we conceptualize reality in terms of opposites, and white can't be black".

 * The complicated explanation is that we may comprehend the problem only as a conceptual problem, like cladists do, and claim that there are two opposite possibilities to discuss reality, both of which are just as consistent given their premises. However, the same "opposite" also exists as a reality (i.e., a fact) in the form of process and pattern, thus suggesting that both of the opposite possibilities to discuss reality is correct at the same time, although they can't be. This is an inconsistency in the concept "correct" between its implications on reality and on conceptualization that we cannot possibly accept, since "correct" has to unify reality and conceptualization. The synthesis of these two meanings of "correct" is accomplished by Aristotle's conceptualization, that is, organizing concepts into genera (genos), specifics (eide) and specific differences (diaphora), that is, differences in similarities. This conceptualization paved the way for science, and is presently attacked by cladism.

 * The fundamental difference between science and cladism is that science is objective and cladism subjective. Science is ambiguous concerning categorization of reality by the simple fact that categorization is ambuguous per definition, and cladism is ambiguous by the fact that it is personal (and thus different between us) Cladism can, however, attract the narrow-minded, like nazism did, and thereby create big problems for science, as well as for humanity. As I see it, there is no room for respect towards cladists, since they do not show any respect towards non-cladists per definition, since cladism is a belief. Non-cladists simply have to continue explaining that cladism is inconsistent (that is, self-contradictory) and empirically erroneous till they have pushed cladists inside a cladistic fence. Non-cladists have to understand that cladists will never abandon their denial of science, since it, for them, would mean denying cladism. (Anyway, thanks Thorwald). Consist, presently at 83.254.20.59 (talk) 22:49, 7 November 2008 (UTC)

 * I can also inform Thorwald that I'm not allowed to make any changes in any article about either cladism or phylogenetics. Instead, I'm constantly blocked by a user named Sjö (appearantly a cladist) and a user named C.Fred (probably not a cladist), although I was passed by a user named Ed.Johnston (appearantly not a cladist). Ed does thus appear to have been transferred from (or voluntarily left)these matters (or this matter). I thus can't change anything in the article. I actually will probably be blocked from this discussion page soon by Sjö. That's how cladists act. Consist, presently at 83.254.20.59 (talk) 23:09, 7 November 2008 (UTC)

Can cladists ever make phylogenetics synonymous to cladistics?
In the beginning of this article about phylogenetics, cladists have sneaked in a sentence synonymizing phylogentics with cladism, which opens for a continuous confusion of these concepts. As explained above, this insneaked synonymonity is just "very nearly". It is just as "very nearly" as apples are "very nearly" synonymous to fruits. This closeness is, indeed, very close. Apples are indeed fruits, but..., are they synonymous to fruits? If they are, what about pears? Aren't they fruits? Cladists "solve" this conceptual problem by "denying" pears. What does this mean? Does it mean that pears aren't fruits, or that they aren't acceptable fruits? Whatever it means, they claim that "evolutionary biologists use the methods and the tools that are useful to laying the evolutionary puzzle, and that in this category [?] does cladism fit" (see Thomas e on the Swedish page on phylogenetics). What category? The evolutionary puzzle is layed by many persons, some of them cladists and some of them non-cladists. How does Thomas e (and the rest of the cladists) mean that non-cladists should react to Thomas e's (and the rest of the cladists') "denial" of us? Shall we just accept it or "deny" cladists? The answer is that facts deny cladism. Cladism is actually an insensible simplification just like nazism or any other -ism is. We don't have to "acknowledge" or "deny" any of them (just as we don't have to choose side in Bush's battle against terrorism), but can instead demonstrate that cladism is inconsistent (thus self-contradictory), and empirically wrong. We don't have to answer their questions, because they simply are insensible. We can continue explaining that their approach is an -ism, that is, one of all possible subjective approaches to reality. We can continue explaining that science differs from all these approaches by being objective. We can admit that objectivity does not allow a single, true classification of reality, but at the same time emphasize the fact that only it agrees with facts. Utopia isn't possible, but science is at least correct. It means that cladists can make phylogentics synonymous to cladistics to the extent that they can make pattern synonymous to process, that is, not. Consist, presently at 83.254.20.59 (talk) 00:20, 8 November 2008 (UTC)

Articles for deletion/Genetic equidistance
Expert opinions on the notability of this topic would be appreciated. Tim Vickers (talk) 16:58, 15 February 2009 (UTC)

How many nucleotides?
In the section "Taxon sampling and phylogenetic signal" there's a number given as "~16,00". Is this a typo, and what would be the sensible number? Expert needed, please! --Stfg (talk) 21:31, 2 June 2010 (UTC)

 * That should be around ~16,000 nucleotides. I've fixed it, and added a reference-- Simon (talk) 00:57, 4 June 2010 (UTC)

proposed addition

 * I would like to propose the following addition:

Phylogeny in Psychoanalysis
Phylogeny in psychoanalysis is the study of the whole family or species of an organism in order to better understand the pre-history of it, because it might have an unconscious influence on a patient,according to Sigmund Freud. After the possibilities of ontogeny, the development of the whole organism viewed from the light of occurrences during the life, have been exhausted phylogeny might shed more light on the pre-history of an organism.

 * However, it would also require a minor edit of the general introduction; into this:

General Introduction
The term phylogenetics derives from the Greek terms phyle (φυλή) and phylon (φῦλον), denoting “tribe” and “race”; and the term genetikos (γενετικός), denoting “relative to birth”, from genesis (γένεσις) “origin” and “birth”. Phylogenetics is the study of evolutionary relatedness among groups of organisms (e.g. species, populations), In biology this is discovered through molecular sequencing data and morphological data matrices, while in Psychoanalysis this is discovered by analysis of the memories of a patient and the relatives.

Phylogenetics/Phylogeny
Are phylogenetics and phylogeny synonymous terms? I have entered the term phylogeny, and have been redirected to phylogenetics, but in the article there is no reference to phylogeny. It all came as I was reading this page http://www.mobot.org/mobot/research/apweb/welcome.html, that uses the term Phylogeny.

Comparison with other Wikipedias:

Catalan W. distinguishes the terms "filogènesi" that is a process, and "filogènia", that is a study or science.

Spanish W. uses the term "filogenia".

French W. uses the term "phylogènie".

Italian W. states that "filogenesi", "filogenetica", "filogenia" are equivalent terms.

I tend to think that "phylogenetics" and "phylogeny" are synonymous, if it is so, it would be useful to include this in the article.--Auró (talk) 19:04, 5 August 2012 (UTC)

 * "Biology online" is clear. Phylogenetics is a science, and phylogeny is the result of this science.--Auró (talk) 20:58, 20 August 2012 (UTC)

Edit 23 September 2012
This article overlapped a lot with Cladistics and Clade, and it still overlaps with Cladogram and probably several others. Having edited Clade and Cladogram, I've tried to make this article more independent of them and more focused on its own topic.

 * Phylogenetic systematics (which redirects to cladistics) isn't a science, it's the application of the science of phylogenetics to systematics by means of the principle that only clades should be named.
 * "Cladism" is pejorative. Bizarrely, it redirected to Phylogenetic nomenclature; this is wrong several times over, so I've changed that redirect to Cladistics.
 * I've replaced the entire sentence that contains the above two points, and which was grammatically a mess, with a sentence that fits better with the preceding one: "The degree to which taxonomy depends on phylogenies differs between schools of taxonomy: numerical taxonomy ignored phylogeny altogether, trying to represent the similarity between organisms instead; phylogenetic systematics tries to reproduce phylogeny in its classification without loss of information; evolutionary taxonomy tries to find a compromise between them in order to represent stages of evolution."
 * I've put "main article: Computational phylogenetics", "main article: Cladogram" and "see also: Molecular phylogenetics" under the headline "Construction of a phylogenetic tree". It's ridiculous, but the cladogram article contains a much more detailed explanation of phylogenetics than the phylogenetics article! I don't have time to move all that stuff now, though. – I seriously wonder whether there should even be a separate article for "cladogram". Doesn't "dendrogram that is the outcome of a phylogenetic analysis" say everything?
 * Do not equate cladogenesis with speciation. They are usually not the same, except under one or two species concepts that (almost?) nobody uses. I have replaced "speciate" by "split".
 * "The problem posed by phylogenetics"... and then a quote about alleged problems with fossils in phylogenetics, from 1967, by two molecular biologists who had almost certainly never tried to do scientific phylogenetics with fossils – AFAIK, nobody did that before the mid-1980s. It was just ridiculous to keep that quote in. There's been a lot of research on that topic in the last 45 years. I've deleted that sentence, which was completely out of context there anyway.
 * Cladistics isn't one method – unless you restrict it to maximum parsimony, which you shouldn't.
 * I've rewritten that paragraph.
 * Phenetics now has its own paragraph. It is, after all, not phylogenetics; it shouldn't be in the middle of a paragraph about methods of phylogenetics!
 * The "Grouping of organisms" section was off topic, and now better explained in the Cladistics article (where it fits just a little better), so I've deleted it.
 * The first paragraph "molecular phylogenetics" section was entirely redundant, so I've deleted it. The second is now in the middle of the introduction, though it should be rewritten for style a bit.
 * Haeckel was completely out of place. I've moved him to the bottom of the article into a new "history of phylogenetics" section and rewritten accordingly.
 * Williamson was completely out of place even within the Haeckel paragraph! Give me a reason to put him back in, and I'll do that...
 * The new "Limitations and workarounds" section contains "homoplasy" (formerly "homoplasy weighting"), "horizontal gene transfer", "taxon sampling", "phylogenetic signal" and "missing data" as subsections.
 * The paragraph about Woese was wrong – rRNA is as prone to long-branch attraction as anything else, and is no longer relied upon to the extent that it once was, so I've deleted the paragraph. Besides, the three domains weren't a theory, but a classification! Woese just elevated the subkingdoms Archaebacteria and Eubacteria to domain status, changing their names to Archaea and Bacteria, because he found them to be so distinct from each other. And a molecular clock is something for divergence dating, not for phylogenetics.
 * "microorganisms, to which the species concept does not apply" – there isn't one species concept, there are 147 (as of February 2008), some of them do apply, and this is irrelevant to phylogenetics anyway! The lack of morphological data that could be used for phylogenetics is real; but because this article already takes molecular data for granted, there's probably no point in stating this. I've deleted the paragraph.
 * Taxon sampling: Wiens (2006) isn't a proposal, it's a demonstration of a fact, using simulations. I've rewritten the sentence; it now cites Zwickl & Hillis (2002) and Wiens (2006) in the same place.
 * The explanation of phylogenetic signal was wrong. I've fixed it. I've also stated explicitly that tests for phylogenetic signal exist – as the reference says.
 * The next sentence, while true, was out of context. I've made the introduction of the limitations section out of it.
 * The first paragraph of the section on the role of fossils is fine, it just needed a bit of modification. The second (which looked very confused to me) was about estimations of diversity rates – that's not phylogenetics, it's an application of phylogenetic trees. If you want to resurrect this, do so in the article about phylogenetic trees.
 * I've mentioned stratocladistics in the last sentence of the section about the role of fossils.

Most sorely missing are more history – I need to track down the reference (a 1998 book by Pascal Tassy) to "phylopessimism", the last stage before phylogenetics became a science – and more references. I can supply all that, but not soon.

There is still too much overlap with several other articles.

David Marjanović (talk) 22:02, 23 September 2012 (UTC)

Taxonomy logically and necessarily includes phylogenetics
Taxonomy is classification and phylogenetics is phylogenetic classification, so phylogenetics is logically and necessarily a subset of taxonomy. The introduction says otherwise and the quote used doesn't even back it up--it says something else nonsensical. Where in the biological literature does it ever say phylogenetics is distinct from taxonomy?

Whether we take the position that taxonoomy is a subset of systematics or vice-versa, phylogenetics would not be distinct from either. Some even equate phylogenetics with systematics, which would mean phylogenetics is a subset of taxonomy or includes it. No matter how you look at it phylogenetics is certainly not distinct from taxonomy.

I have made the correction twice but it was reverted each time.--Trouveur de faits (talk) 15:28, 4 July 2013 (UTC)
 * Your statement that "phylogenetics is phylogenetic classification" appears to me to be the heart of this problem. One can derive a phylogeny without creating a classification from it, in fact this is a common approach because (1) a phylogeny is likely to come out differently with the next analysis that is based on different or greater amounts of data and (2) conflicting phylogenies are often produced for the same group of organisms if different loci are used or if organelle DNA is compared with nuclear DNA. Some cladistic practitioners are fond of stating that a phylogeny is a hypothesis, it is always challenged by the next phylogenetic analysis of the same organisms. Classification is a later step, a step that takes into account how the classification is to be used, and makes decisions that compensate for the lack of absolutely complete data (because data are never absolutely complete). Sminthopsis84 (talk) 18:26, 4 July 2013 (UTC)
 * Precisely my view. However, sources express different opinions as to the meaning and relationship of these topics (phylogenetics, taxonomy, classification, systematics). Our task is to fairly represent all of these opinions where they are sufficiently represented in reliable sources, regardless of whether we think they are right or wrong. It's difficult to do, and tends to produce confusing text unless carefully written, but we cannot simplify or impose our views.
 * I do agree that the Edwards & Cavalli-Sforza quote doesn't support the sentence in the lead. I don't have access to the source so can't tell if it's just the quote that is poor or the source as a whole. But the sentence "Taxonomy, the classification, identification, and naming of organisms, is usually richly informed by phylogenetics, but remains methodologically and logically distinct" can, I think, be sourced from the literature. I'll see if I can find a better ref. Peter coxhead (talk) 10:21, 5 July 2013 (UTC)
 * I'd like to comment further on Trouveur de faits's statement above.
 * Taxonomy is classification. See Taxonomy (biology) for sourced alternative definitions. Some support this statement, some do not. In particular, for those who define taxonomy as including description, identification and nomenclature it's clearly not the same as classification. Alpha taxonomy is largely independent of classification.
 * phylogenetics is phylogenetic classification. Says who? Many different classifications can be derived from the same phylogenetic tree. They can be based on the traditional rank-based codes, nowadays generally using strictly monophyletic taxa as in the APG systems, but some also using paraphyletic taxa as in Stace's system for the British flora. They can alternatively be based on the Phylocode. So how can phylogenetics and phylogenetic classification be the same thing? Maybe some sources say they are, but others clearly describe a two-step process: first obtain phylogenetic hypotheses (e.g. trees) and then decide on a classification.
 * Peter coxhead (talk) 10:58, 5 July 2013 (UTC)

You're making artificial and gratuitous distinctions. A phylogeny is a classification, whether or not it is contradicted by another analysis. The 2-step process you describe is the process of phylogenetic classification. You could nitpick and say there's the phylogeny and there's the classification, but if you do, phylogenetics still necessarily includes both.

" 'Phylogenetics is phylogenetic classification' Says who?" Professional taxonomists, that's who. I quote from Cladistics, 1st ed., p. 3:

"In biology, cladistics is a method of systematics (Patterson, 1980), most coherently formulated by Hennig (1950, 1966), which is used to reconstruct geneologies of organisms and to construct classifications. However, it is also a general approach to classification which can be used for comparative information, having been independently discovered in linguistics..." This clearly says classification is part and parcel of phylogenetics. You'll never find any reference that says the 2 are distinct.--Trouveur de faits (talk) 17:13, 6 July 2013 (UTC)
 * Please give better hints about citations, to save other editors from pointless trips to the bookshelf to check this book, and possibly others with the same first word in the title.
 * Now to your point: "method A is used to make classifications" does not mean that method A is itself classification. Your interpretation of the words is incorrect. Counting the number of hairs on the backs of flies is a method that could be used to make classifications, but it is not itself classification in any meaningful sense. Classifying flies only according to the number of hairs on their backs would be neither generally useful to those who want to distinguish different fly species nor a biologically realistic classification. Similarly, constructing a phylogeny from the nuclear gene pCOSAt103 may not give a useful representation of the evolutionary history of the taxa concerned, nor is it likely to indicate where the boundaries should be drawn between the taxa. Drawing the boundaries between taxa is part of classification, but phylogenetic taxonomists either take that as already provided by previous generations of scientists, or impose the boundaries after they have seen the phylogeny. Classification is an aim for which phylogenies are one tool that is used. To use your idiomatic phrase, phylogenetics is part and parcel of classification, not the other way around. Sminthopsis84 (talk) 22:39, 7 July 2013 (UTC)

"phylogenetics is part and parcel of classification," also proves my point that phylogenetics and taxonomy are not distinct. We don't say that oranges are distinct from fruits nor vice versa. Method A is a necessary part of the classification. You can't have a phylogenetic taxonomy without a phylogeny, nor can you have a phylogeny without a phylogenetic taxonomy. Like I say, you are nitpicking and making arbitrary, artificial, and gratuitous distinctions, and disagreeing with professional taxonomists.--Trouveur de faits (talk) 14:36, 8 July 2013 (UTC)

 * Of course "oranges are distinct from fruits". Oranges are a subset of fruits (using the normal English sense of the word "fruit"). A subset is, by definition, not the same as (i.e. is distinct from) the set of which it is a member.
 * No-one says that phylogenetics, classification and taxonomy are unrelated, but this doesn't mean that they are the same thing. Classification and taxonomy existed before (formal) phylogenetics; if nothing else the "history of biological classification" and the "history of taxonomy" are not the same as the "history of phylogenetics". You clearly "can't have a phylogenetic taxonomy without a phylogeny", as you say, but you can have a "bare" phylogeny, e.g. a cladogram showing the relationship between species in which none of the other nodes are named and which is not used to inform classification. These are necessary distinctions between three topics which are (today) closely related but which are not identical. Peter coxhead (talk) 19:12, 8 July 2013 (UTC)

To say a phylogeny is not a classification is irrational and you'll have to provide a reference which reflects that view and that has some kind of currency instead of just a small minority view.--Trouveur de faits (talk) 15:24, 15 July 2013 (UTC)
 * Well, consider this quotation from Mishler (2009), Taxon 58: 61–67: "The major outcome of the evolutionary process is the production of an ever-branching phylogenetic tree of life ... most systematists now feel that the general biological classification system should be used to reflect this tree of life." The classification should the phylogenetic tree of life, but it's not the same thing.
 * Botanists (biologists generally) have never been very interested in talking about theory (unlike, say, physicists), so you often have to infer meaning from usage. Consider Note that the very title implies that "a molecular phylogeny" isn't a "classification". If you look at p. 82, the phylogeny is the tree on the left; the classification is the set of labels on the right.
 * I couldn't find anyone who says without qualification that a phylogeny a classification – do you have a source for this? Peter coxhead (talk) 15:40, 15 July 2013 (UTC)

"1st evolutionary tree", Ernst Haeckel (1866)
I understand that Haeckel's tree is likely the first, out side of Darwin's notebook, meant to imply continuity in the lineage of life but I feel that it is somewhat dishonest to label it the "1st" evolutionary tree. This is primarily because it doesn't include any paleontological data and is not the first to show continuous branching. As outlined [| on this page], Haeckel's diagram is preceded by both that of Lamarck, Hitchcock, and Bronn, (of which the latter two paired their trees to paleontological scales). Additional information about each can be found in this essay1, by JD Archibald. I would contend that as both Darwin and Haeckel failed to provide a mechanism by which heredity functioned, we should consider one of the these earlier "trees" as being "the first". Seeing as Hitchcock was vehemently anti-evolution and Bronn explicitly excluded a mechanism for the succession of forms that he documented, I recommend that Bronn replace Haeckel in this sense. In addition, Bronn was correspondent with Darwin and the translator of OOSMNSPFRSL into German 2. Any thoughts or objections to my proposed change? StereoTypo (talk) 04:07, 7 April 2014 (UTC)

Earth and life
Domain of crocodile 216.247.81.103 (talk) 22:55, 23 January 2023 (UTC)

Basic grammar
What's with specie's? It should be species' for both singular and plural possessives, as species is both the singular and the plural. Aboctok (talk) 03:38, 25 April 2023 (UTC)
 * has been fixed. Peter coxhead (talk) 09:45, 27 April 2023 (UTC)

Plagiarism Issue
Certain sections of the page, particularly "Phylogenetic screens" and "Phylogenetic tree shapes", seem to have been copied from this paper. I wasn't sure if reporting that section would affect the entire article so I wanted to raise that concern here. — Preceding unsigned comment added by Reputationbiohazard (talk • contribs) 15:25, 15 February 2024 (UTC)

title: Talk:Phylogenetics


text:
Talk:Evolutionary developmental biology

No Mention of Turing?
I wanted to refresh my memory on Turing's contribution to this field. My understanding is that he and I believe D'Arcy Thompson wrote at least one paper where they essentially mapped out some of the core ideas: that constraints from math, physics, etc. shaped the type of phenotypes that could result from changes to genotype. I may be saying that wrong, Biology isn't my field, but I know I've seen several mentions that Turing wrote about the basic ideas of evo-devo many years before it was rediscovered and became an active field of biology. MadScientistX11 (talk) 16:01, 14 May 2023 (UTC)

 * Turing wrote a paper on how in theory patterns (in fur or feathers) could appear. Much later, evo-devo found that he'd broadly guessed correctly. Thompson (already in the article) didn't believe in evolution, which could be seen as a small problem in making him a father of evo-devo; he wanted to show that body shapes arose spontaneously, rather than through biochemical mechanisms under natural selection. I suppose if we're going to go back to the beginning, whatever that is, we'd start with Aristotle, who speculated that bodies come into being through a selection of parts; this most likely meant embryonic development (ontogeny) not phylogeny, i.e. after conception the appropriate parts are selected (from some non-physical space?) and assembled. I'm not sure any of this is exactly evo-devo, more the history of biology, but perhaps a brief paragraph of 'Precursors' or 'Historical background' would not go amiss. Chiswick Chap (talk) 18:15, 14 May 2023 (UTC)

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

title: Talk:Evolutionary developmental biology


text:
Talk:Political Soldier

Page Move
This article was at Politcal Soldier. Political was spelled incorrectly. I have moved the page. - iHoshie 10:46, May 8, 2004 (UTC)

"Evola, an Italian fascist philosopher"
I have once again removed this improper characterization. Here are a few relevant quotes:

''"As we have seen, Julius Evola, who might conceivably be counted among them--was not a "fascist" thinker in any meaningful sense of the term. He himself, both implicitly and explicitly, rejected such a characterization. That he remains identified as a fascist thinker by many contemporary commentators tells us more about contemporary discussions than it does about Fascism." '' Mussolini's intellectuals: fascist social and political thought p. 250

''"Whomever he influenced, he influenced them with doctrines that could only be characterized as "Traditional"--certainly not Fascist." "Evola was not a Fascist thinker, so it would be hard to imagine that his ideas might be "quintessentially" Fascist."'' The search for neofascism p.108

''"Whatever the influence of Evola on the antidemocratic thought of Western and Eastern Europe, it cannot be classified as 'fascist' or 'neofascist'" It is at best an expression of that traditional reactionary thought found among those thinkers who, in the first years of the nineteenth century, sought the restoration of a Europe that preceded the French Revolution--or, preferably, a world that preceded the Renaissance. None of this tells us anything about Fascism.'' Fascism: The nature of fascism p.340 Posted by Pollinosisss 15:35, 2 January 2010

 * Some nice quotes, though author's names would help other editors. It is not sufficient to make edits with the rationale you gave "It is my understanding that Evola was not a Fascist in any meaningful sense of the word" - That is original research/opinion, so your quotes are most welcome, though none of them is exactly deinitive; at best they are equivocal. Unfortunately, I do not currently have access to my sources, but the Wikipedia article on Julius Evola is less equivocal. Forgive me quoting Wikipedia (!), but the article itself is well-sourced:

 * "In the late 1920s, Evola expressed his support for a radical Fascist revolution to sweep modern Judeo-Christianity out of Italy...."
 * "...he hoped to influence the Mussolini regime toward his own variation on fascist racial theories..."
 * "From 1934 to 1943, he edited the cultural page of Roberto Farinacci's journal Regime Fascista."
 * "Evola later recounted that Mussolini had found in his work a uniquely Roman form of fascist racism distinct from that found in Nazi Germany"

 * and there are many others. In addition, it is worth noting that Evola is listed under the category "Italian neo-fascists". It is undoubtedly the case that he was never a member of Mussilini's Fascist party, but that does not mean he was not a fascist. Emeraude (talk) 16:19, 2 January 2010 (UTC)

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title: Talk:Political Soldier


text:
Talk:Selection (biology)

Article should be merged
with Natural selection ?

I came across this article today and I really don't understand why it exists. It should be deleted - the Natural selection article already covers this topic and it is cited. I see the figure by User:Duncharris that schematically classes Selection above natural vs. artificial selection. However, there is no citation to back the conceptual notion - at best this should be a footnote on the natural selection page and treated separately. I have never encountered it in my studies and reading on evolution. Unless this can be backed up by some external peer-reviewed or expert opinion - I vote this page be merged or removed. Thompsma (talk) 23:19, 10 September 2009 (UTC)
 * I agree. Why has this not been merged yet??? Peteruetz (talk) 15:05, 4 March 2014 (UTC)
 * Since this has been unopposed since 2009, and nobody has objected to the proposal at the target article, I have now created the redirect. Chiswick Chap (talk) 05:40, 28 August 2016 (UTC)

Comment on the chart
In the chart, "natural selection" is subdivided into two subcategories: ecological selection and sexual selection. Shouldn't a third subcategory be added: kin selection? EPM 17:31, 24 February 2006 (UTC)

Ecological selection
I'm not satisfied with ecological selection. I think the selection page etc over-represent ecological selection as a category, and incorrectly classify sexual selection as a sub-category of natural selection. IMHO, natural selection and sexual selection are thought of as two distinct processes by practitioners within the field, with natural selection occupying the position in the figure in selection that is currently occupied by ecological selection. At least, some references should be added to selection and ecological selection to support the views presented and some historical information should be added to trace the change from Darwin's view to the one presented here. Pete.Hurd 19:47, 10 August 2006 (UTC)

And I'm not really satisfied with artificial selection! As I've said over on the natural selection page I feel artificial selection is a special case of natural selection i.e. a subset (as long as we are talking about biological entities differentially reproducing). Sober seems to agree...

 * Artificial selection is not selection that takes places outside of nature, but selection that occurs within a particular niche found in nature. The [Waddington] experiment involved the interaction of members of one species with members of another. The fact that one of those species happens to have been Homo sapiens sapiens does not affect the point. Artificial selection is a variety of natural selection; the relation is one of set inclusion, not disjointness.

— Axel147 00:35, 12 August 2006 (UTC)

 * Agree - one could/shoud rather distinguish between interspecific/between-species selection (ecological selection as usually understood + some cases of artificial selection, such as domestication of horses vs non-domestication of zebras) and interspecific/within-species selection (sexual + kin + most artificial selection). The former is more relevant in a macroevolutionary context, while the latter is more of a factor in speciation and adaptation on the species level (although in eusocial hymenopterans, it is of considerable macroevolutionary importance too). The evolutionary significance is that the former pits unconnected gene-pools against each other and the latter occurs within the same gene pool. darwin inintially started with studying artificial selection, and then (in "Origin of Species") expanded his view on interspecific selection, whereas Wallace directly discussed the latter.
 * Of course a clean line cannot be always drawn as evolution is an ongoing process. But most cases of evolution yielding to selective forces can be clearly attributed to one or the other being predominant. For example, the showy plumage of some male birds of paradise could of course not evolve beyond a point where it was detrimental to their survival (in Megaceros, changing climate and thus vegetation actually shifted the balance so that a sexually-selected character became detrimental to their survival). But the initial evolution of an exaggerated sexual trait was in both cases driven by intraspecific selection.
 * Indeed, the article should be somehow fused with Natural selection. Probably best merged into it (be aware that this will involve a fair amount of redirect-checking if in the course of this "selection" becomes a pure disambig page). "Selection" is the general term for any process of choosing and discarding from a set of possibilities. "Natural selection" is when this process occurs in nature. The point above about the "nature vs humans" division being artificial is very correct indeed. Evolutionarily, humans putting out food for their Old German Owl pigeons in their cage is just the same as Angraecum sesquipedale evolving a longer and even longer spur in its flowers, which it could because there was already Xanthopan morgani to "run-away" with: provision of a food resource under conditions where it is accessible to a part of a gene pool, bearing a particular character, that otherwise would have been in dire straits.
 * It does not need intelligence for evolution to work; centuries of a loose "best-fit" trial-and-error just do the job as well as human planning does (arguably better in fact, because it gets to try out more options), and from the evolutionary perspective of the lineages selected upon, it is all the same - they either thrive or fail. And the pigeon fancier's taste of what constitutes a desirable breed is in fact co-evolution between the humans who like a particular sort of pigeon and those strange birds which are thus able to thrive though they'd soon die outside human care. Dysmorodrepanis 15:42, 2 December 2006 (UTC)

The unit of selection
It seems to me as if no distinction is made between selection on the genetic level or on the level of individuals. I think this is important because Fisher's fundamental theorem of natural selection seems to be dubious. The reason seems to be that the mean fitness is determined as mean over the set of genes, assuming that a gene may have a fitness of its own.

On the other hand, if we assume that the selection of individuals rules the enrichment of genes in a large population and determines the mean fitness over the set of individuals we may for instance get the theorem of gaussian adaptation leading to quite different properties of evolution.

Kjells 11:06, 21 February 2007 (UTC)

 * Perhaps some reference to the Unit of selection article would help. Pete.Hurd 16:42, 21 February 2007 (UTC)

Se for instance: Dawkins, R. The Selfish Gene. Oxford University Press, 1976.

More references may be found on my web site:

http://www.evolution-in-a-nutshell.se Kjells 10:23, 22 February 2007 (UTC)

Merge from evolutionary pressure
I've suggested evolutionary pressure be merged into this article. This one is quite short itself, and evolutionary pressure is no more than a stub. Any arguments in favour of keeping it separate? If it can be developed more there's always the possibility of splitting it off in future. Richard001 01:33, 16 September 2007 (UTC)

 * Disagree. I believe that the Evolutionary Pressure article deserves to be extended and a seperate entity from the main article on selection.Zisimos (talk) 20:35, 7 May 2008 (UTC)

You need to be careful on how you word evolutionary processes, as a species does not "adapt" to selective pressures and it shows a fundamental misunderstanding of evolution. Things do not evolve or change due to selective pressure, that is not how natural selection works, that is "Dawkins Evolution" and it is falseDirtclustit (talk) 07:39, 7 September 2013 (UTC)

disambiguate from selection in computing
(I'm not sure how to link to wikipages with parentheses) discusses "focus" in computing. "Selection" is related to "focus" in subtle ways and should be discussed in Wikipedia. Recommend disambiguation page under "selection" which, for now, can link to focus (computing) page. Rokahn (talk) 19:00, 10 February 2008 (UTC)Rokahn

Pragmatics...? (overview)
Who put that there? It doesn't make sense with the sentence to me. What do you think of it? 76.70.89.203 (talk) 00:16, 12 February 2009 (UTC)

The term "selection" is not scientific
Scientists should definitely avoid religious and anthropomorphic terms like "selection" (etc.) altogether (e.g., "God has selected the Jews as the foremost people among peoples"). Instead, selective processes in "nature" can be replaced by stabilization processes on all biochemical and populational levels, from genomic stability up to sociological and political stabilities (only some populations will have enough stability through time, depending on fast shifting environments; and some populations are so instable, that they die out). --- OE, Feb 2010 —Preceding unsigned comment added by 131.152.209.90 (talk) 16:16, 11 February 2010 (UTC)

Selection defined by who?
According to which person?

 * In the context of evolution, certain traits or alleles of genes segregating within a population may be subject to selection. Under selection, individuals with advantageous or "adaptive" traits tend to be more successful than their peers reproductively—meaning they contribute more offspring to the succeeding generation than others do. — Preceding unsigned comment added by 196.210.253.89 (talk) 16:17, 26 August 2011 (UTC)

Requested move 29 May 2015

 * The following is a closed discussion of a requested move. Please do not modify it. Subsequent comments should be made in a new section on the talk page. Editors desiring to contest the closing decision should consider a move review. No further edits should be made to this section.

The result of the move request was: MOVED - to Selection (biology) as unanimously supported after a full relisting period. <<< SOME GADGET GEEK >>> (talk) 01:36, 27 June 2015 (UTC)

– Unanimous agreement to the "out of process" discussion at Talk:Selection (disambiguation), as requested there by closer. Relisted. Jenks24 (talk) 18:07, 18 June 2015 (UTC) <<< SOME GADGET GEEK >>> (talk) 02:08, 29 May 2015 (UTC)
 * Selection → Selection (genetics)
 * Selection (disambiguation) → Selection

 * Thanks. I think the first step is worthy of careful discussion, particularly since the concept of selection in genetics has been at Selection since 2003. It should not be moved without some discussion of whether it is, in fact, the primary topic of the term. The Selection (disambiguation) page lists a total of fifteen senses, but some of these are partial title matches (Selection algorithm, Selection-based search, and Selection effect) which might not actually be referred to just as "Selection", some are otherwise not matching titles (Selected (album), Selective school, The Selection, and Selektion). With respect to those that are exact title matches - Selection (genetic algorithm), Selection (user interface), Selection (relational algebra), Selection (Australian history), Selection (album), and a Metro Inc. store brand - I am not sure that any of these, or all of them put together, are comparable to the natural history sense in terms of long-term historic importance. I am also not sure that Selection (genetic algorithm) is not a subtopic of selection (in the genetic sense) generally. At least some evidence should be presented to determine that a topic of substantial historical importance is not the primary topic for a longstanding title. Cheers! bd2412  T 03:23, 29 May 2015 (UTC)

 * Strong support per the last move request; "selection" is not restricted to genetics, and selection effects in science are not restricted to evolution. Indeed selection is a key concern in statistics. -- 65.94.43.89 (talk) 04:12, 29 May 2015 (UTC)
 * The article on that would appear to be Selection bias (on the page as Selection effect). Is this commonly referred to as just "selection"? bd2412  T 04:22, 29 May 2015 (UTC)
 * "Selection" means the act of selecting or choosing, and happens in many places, not only genetics. Anthony Appleyard (talk) 04:53, 29 May 2015 (UTC)
 * - are we missing a potentially useful WP:DABCONCEPT article on the concept of selection, then? bd2412  T 12:22, 29 May 2015 (UTC)
 * Suggest Selection (evolutionary biology). Selection was occurring within biology long before the concept of genetics was developed.  The concept of selection may also be confused with processes utilised by genetic scientists or also with topics such as Selection (genetic algorithm). GregKaye 05:04, 29 May 2015 (UTC)
 * Support move to "Selection (biology)" per the last move request Red Slash. Khestwol (talk) 08:10, 29 May 2015 (UTC)
 * Support Selection (evolutionary biology). Rreagan007 (talk) 01:57, 12 June 2015 (UTC)
 * Relisting comment. Seems clear there's a consensus to move, but not sure we've got a consensus on which disambiguator ("genetics" or "evolutionary biology") to use. Jenks24 (talk) 18:07, 18 June 2015 (UTC)
 * Oppose (evolutionary biology). Selection (biology) is available and as far as I can tell, unambiguous. Red Slash 19:08, 18 June 2015 (UTC)
 * Comment, I think "Selection (biology)" might be better option. Khestwol (talk) 19:52, 18 June 2015 (UTC)
 * Support Selection (biology). Best, FoCuSandLeArN (talk) 22:47, 18 June 2015 (UTC)

 * The above discussion is preserved as an archive of a requested move. Please do not modify it. Subsequent comments should be made in a new section on this talk page or in a move review. No further edits should be made to this section.

title: Talk:Selection (biology)


text:
Jabba

Jabba may refer to:

 * Jabba the Hutt, a fictional character in the Star Wars franchise
 * Jabba (presenter) (Jason Davis, born 1973), Australian actor and media personality
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 * Jabba language, or Hyam language

title: Jabba


text:
Talk:Mutation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Material to integrate into target article
 * germline mutation

Material to carve off into a separate article
 * compensatory mutation

Lede

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

Overview

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

Causes

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

Spontaneous mutation

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

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

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

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

Classification of types

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

By effect on structure

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

By impact on protein sequence

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

By effect on function

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

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

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

By inheritance
Germline mutation.

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

Special classes

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

Nomenclature

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

Mutation rates

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

Randomness of mutations

 * nothing necessary here

Disease causation

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

Inherited disorders

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

Role in carcinogenesis

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

Prion mutations

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

Beneficial mutations

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

Compensated pathogenic deviations

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

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

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

title: Talk:Mutation


text:
Salim Joubran

Salim Joubran (سليم جبران, סלים ג'ובראן; 1947 – 15 March 2024) was a judge of the Supreme Court of Israel. He served as a Supreme Court justice from 2003, and became a permanent member in May 2004. Joubran was of Christian Maronite heritage and affiliated with the Arab Christian community. Joubran was the first Arab to receive a permanent appointment in the Israeli Supreme Court. He was also described as the second Arab judge to hold a Supreme Court appointment, preceded by Abdel Rahman Zuabi, who held a fixed nine-month appointment in 1999.

Biography
Salim Joubran was born in the German Colony neighborhood of Haifa, Mandatory Palestine, to a Christian family of Maronite Lebanese origin.

Joubran graduated from the Terra Santa School of the Franciscan Order in Acre. He earned a law degree from the Hebrew University of Jerusalem and entered private practice as a lawyer in 1970.

Joubran has four children, three of whom are lawyers. His son Charbel is a lawyer in the field of sports and represents football players in Israel and abroad.

Joubran died on 15 March 2024, at the age of 76.

Legal career
In 1982, Joubran left private practice after 12 years to accept an appointment as a judge on Haifa's Magistrate's Court, where he served for 11 years. In 1993, he was appointed to Haifa's district court, and served in that capacity for another 10 years, following which he was elevated to the Supreme Court first as a temporary and then as a permanent judge.

Joubran was an expert on criminal law. He was also the first Arab to chair the Central Elections Committee. In the 2013 Israeli municipal elections, he barred the national ruling party Likud's advertisements for being "racist and almost certain to hurt the feelings of Arab Israelis and disrupt public order". This also overruled the advice of Attorney General Yehuda Weinstein, who suggested the committee had no authority to regulate online advertisements and posters.

Joubran was appointed justice in the Supreme Court of Israel in 2004. He was appointed deputy to the Supreme Court chief justice on 12 June 2017. He retired later in 2017, having reached the mandatory retirement age of 70.

Academic and public positions
Joubran was a lecturer at the Law Faculty at the University of Haifa. He served as governor of Israel Rotary (dist. 2490), and chairman of the Zeltner Fund for legal research sponsored by Rotary Israel and Tel Aviv University.

title: Salim Joubran


text:
Mutation (disambiguation)

A mutation is a change in the sequence of an organism's genetic material.

Mutation or mutate may also refer to:

Film, television, and literature

 * Mutation (novel), a 1990 medical thriller by Robin Cook
 * Savage Land Mutates, a group of mutants in Marvel Comics
 * Human Mutation, a peer-reviewed medical journal of human genetics
 * The Mutations, a 1974 British horror film, also released as The Freakmaker
 * The Mutation (novel), a book in the Animorphs series, by K.A. Applegate
 * “Mutations”, an episode of The Good Doctor

Music

 * Mutation, the process of changing hexachords in medieval music theory
 * Mutation (organ stop), a type of organ stop that does not sound at unison or octave pitch
 * Mutations (Beck album), 1998
 * Mutations (Fight album), 1994
 * Mutations (Vijay Iyer album), 2014
 * Mutations EP, 1992 EP by Orbital
 * Mutate (album), 1993 album by Battery
 * "Mutations", a song by Salt the Wound from their 2009 album, Ares
 * Mutation, a 2005 album by Donna Williams

Sciences

 * Mutation (genetic algorithm), an operator in a genetic algorithm of computing
 * Mutation (algebra), an operation on algebras producing an algebra with a modified multiplication operation
 * Mutation (knot theory), an operation on a knot that creates different knots
 * Mutation (Jordan algebra), an operation on Jordan algebras that creates different Jordan algebras
 * Mutation of a seed, in the theory of cluster algebras
 * Apophony, in linguistics, a change in a sound in a word
 * Consonant mutation, in linguistics, a change in a consonant sound
 * Affection (linguistics) or vowel mutation, the change in the quality of a vowel under the influence of the following vowel in Celtic languages

Other

 * Voice change, the change in human voice during puberty
 * Mutation, division and transfer of land ownership in India; see Village accountant

title: Mutation (disambiguation)