Talk:Phylogenetics

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On 28 Mar 2005, this article was nominated for deletion. See Wikipedia: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? [1]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)

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)