Talk:Cladistics/Archive 2

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Archive 1

Archive 2

Archive 3

Archive 4

Should there not be explicate discussions of outgroups in this articles. This is important since it allows the making of rooted cladograms instead of mere unrooted ones. MichaelSH 13:58, 2 October 2005 (UTC)

Definitely --Aranae 04:40, 3 October 2005 (UTC)

In a strict definition a cladogram always has a basal outgroup.Valich 02:18, 10 April 2007 (UTC)

Cladistics is currently undergoing a review to see if it should remain a Featured Article. See Wikipedia:Featured_article_review/Cladistics for the comments that have been made.

I sympathize with many of the comments, and I have changes in mind to improve the article, but I want to check here to see if any of my changes would be accepted by the other editors. The things I believe I could help with are 1(c) 'factually accurate', 2(a) 'concise lead section', 2(c) 'substantial table of contents', and 4 'appropriate length, staying focused, without unnecessary detail.' Crzycheetah listed all of these as FA requirements he felt the article does *not* meet, in his comment of 14-Dec-06 in the above-mentioned review.

Starting with the most controversial change, I'd like to replace the lead paragraph. It is too oracular, making it sound as though cladistics is simply the correct way of studying relationships between organisms. Cladistics (in my view) is a school of thought that has enlivened a number of taxonomic questions, and has a body of controversies associated with it. I'd like to include only material in the new lead paragraph that can be fully cited.

Later in the article, there is heavy use of special technical terms whose definitions are rather 'squishy', although they might be tightened up by appropriate citations. I hope this article would only extend itself to cover those terms that it could adequately expound and explain. It's my guess that Crzycheetah may have been thinking of the exotic technical terms in his complaint about FA criterion 4, 'without unnecessary detail'. It's possible some sub-articles might be needed to fully explain the terminology of cladistics. It would be especially helpful to give examples where cladistics would give different guidance than other approaches to systematics. Clear definitions of terms are always good.

This article at present has seven references (that may be perfectly good references) but they are not cited in the text. Curiously, Willi Hennig is not in the reference list. He also should be cited in the text.

Please let me know your thoughts. EdJohnston 19:52, 11 January 2007 (UTC)

I know I already mostly bowed out of this one, but the last time an established editor made a content change to this article was in October. It's essentially unwatched except for FAR reviewers; since you have some specific ideas on how to improve the article, you can probably go right ahead. Opabinia regalis 01:34, 12 January 2007 (UTC)

Thus encouraged, I went ahead and converted the references to template form. Added ISBNs and PMIDs. Let me know if anyone prefers the old format for the references. EdJohnston 03:37, 12 January 2007 (UTC)

As part of the FAR improvements, I'm hoping to provide citation for every controversial statement. Some of the plain narrative of the cladistic approach seems harmless, but there are other passages that appear to come out of nowhere. I wonder if anyone can think of a source for the following items? (One of the FAR reviewers already asked about the 'basal' stuff).

1. THIS SEEMS CURIOUS, and I'm not even sure that it's a core cladistic belief:

Several more terms are defined for the description of cladograms and the positions of items within them. A species or clade is basal to another clade if it holds more plesiomorphic characters than that other clade. Usually a basal group is very species-poor as compared to a more derived group. It is not a requirement that a basal group is present. For example when considering birds and mammals together, neither is basal to the other: both have many derived characters.

2. THE CLAIM THAT Maximum Likelihood is non-Hennigian seems unusual: (FAR reviewer Aranae commented on this):

As DNA sequencing has become cheaper and easier, molecular systematics has become a more and more popular way to reconstruct phylogenies. Using a parsimony criterion is only one of several methods to infer a phylogeny from molecular data; maximum likelihood and Bayesian inference, which incorporate explicit models of sequence evolution, are non-Hennigian ways to evaluate sequence data. Another powerful method of reconstructing phylogenies is the use of genomic retrotransposon markers, which are thought to be less prone to the reversion and convergence that plagues sequence data.

I agree that parsimony is distinct from ML and Bayesian, but the latter two analytical techniques still focus on shared derived characters and are therefore descended from Hennigian/cladistic philosophies and warrant discussion in the article. I would be surprised if a large majority of the field would agree with the statement that ML is non-Hennigian. Some certainly would, but definitely not all and probably not most. --Aranae 06:02, 22 January 2007 (UTC)

3. SEEMS LIKE A VERY IMPRESSIONISTIC GENERALIZATION (needs a citation if true):

Ideally, morphological, molecular and possibly other (behavioral etc.) phylogenies should be combined: none of the methods is "superior", but all have different intrinsic sources of error. For example, character convergence (homoplasy) is much more common in morphological data than in molecular sequence data, but character reversions are more common in the latter (see long branch attraction).

4. PROBABLY IS TOO SWEEPING: (It is harmless to apply cladistics to textual analysis, but 'cladistics does not assume any particular theory of evolution' would need to be cited, preferably to Hennig).

Cladistics does not assume any particular theory of evolution, only the background knowledge of descent with modification. Thus, cladistic methods can be, and recently have been, usefully applied to non-biological systems, including determining language families in historical linguistics and the filiation of manuscripts in textual criticism.

If anyone knows a citation that will help with items 1-4, I'd appreciate it. The alternative is probably to remove the uncitable claims. EdJohnston 01:00, 15 January 2007 (UTC)

I can't see that we need a Clade article separate from this one. I'm not even sure it contains any information that this article doesn't. Comments? --HughCharlesParker (talk - contribs) 10:22, 1 February 2007 (UTC)

Agreed. I can't think of any situation in which someone would want to read about clades independently of cladistics. In a sense, cladistics is clades. Geoff 02:49, 14 March 2007 (UTC)

A clade is simply a group of organisms that share a common ancestor. In this respect it can be applied to both phylogenetic trees as well as cladograms. For example, in a purely phylogenetic analysis the order Carnivora are considered to be a monophyletic clade - a crown-clade - whether it is viewed in a phylogenetic tree analyses or a cladistic phylogenetic systematics analyses. I think there should be reference to it here in the cladistics article, but still kept as a separate article because it is sometimes used in other contexts. I do, however, see where there might be opposition to this view.Valich 05:43, 8 April 2007 (UTC)

With no reference to cladistics the Cimolesta article reads: "The Cimolesta contains several groups that are very different from each other, and are sometimes regarded as separate orders (which makes the Cimolesta a clade between that of order and superorder)." It is referred to phylogenetically and taxonomically as a "clade" because there is no other suitable word to use here.Valich 02:22, 10 April 2007 (UTC)

By calling the Cimolesta a clade, you would surely be implying that they all have a common ancestor. Is this actually known? I observe that our Cimolesta article has no references, so I'm not sure how seriously to take it. A Google search returns a site with this wonderful phrase: 'Problematic, some consider this a wastebasket taxon'. Most likely there are other groups that might illustrate your idea, though.

The key point of cladistics as a philosophy of classification, I have read, is to insist that all classification be in terms of clades. EdJohnston 02:56, 10 April 2007 (UTC)

By calling Cimolesta a clade, they are using the term in an ambiguous sense, that certainly does not correspond to a cladistic's analyses. Wouldn't you agree? The point I was trying to make, and I admit that it was a poor example, was that the term "clade" does not just refer to cladistic analysis. I updated the clade article to reflect this point. Please edit it accordingly. I think the current cladistics article should have a better introduction that corresponds to Hennig's phylogenetic systematics, and should emphasize the importance of having a basal outgroup when constructing a cladogram. This important topic is neglected in the article. Further, most all conventional "cladograms," in contrast to phylogenetic trees, are still based on morphological traits, or as Hennig called them, "apomorphic characters."Valich 06:12, 10 April 2007 (UTC)

I don't object to including the term 'basal outgroup.' However, the previous FA version of Cladistics had almost no references for its claims, it didn't even have a work of Hennig in the reference list. I hope any definitions we provide in the new version can be fully cited. EdJohnston 18:01, 10 April 2007 (UTC)

If you'd like, I can dig up my sources on this and let you know more about Hennig's major contributions. Afterall, he is the founder of cladistics, only he called it phylogenetic systematics back then in the 50's. It was, and usually still is, traditionally based on morphological traits, or as he called them, "apomorphic characters." Mention should also be made of the once rival "phenetics" approach - although this has now come under disfavor - and how phylogenetic cladistics are now being based on molecular data rather than morphology, but in many cases still seem to produce somewhat the same results. Molecular analysis should be a sub-category in the article because there's a lot to describe here: DNA sequencing, karyotype analysis, Bayesian analyses - Bayesian trees, Maximum parsimony (MP/MRP), Bootstrap support (MP BP topology), IRBP trees, ML topology (see Flynn et al. 2005, etc.). This is what they're using now to construct cladistic trees. I could put together a short paragraph on this to introduce the reader, with links, but not right now. I'll work on the clade article in the next few weeks and use it to introduce the terms "grade" and "tribe," which are also commonly used in phylogenetics. The term clade is used as am alternative due to the inconsistencies that occur when taxonomically labelling an extinct species as being in this or that family and subfamily and then later discovering that they were descended from the same species. By grouping them into a clades, then subclades and sometimes tribes, this avoids the confusion in using the static taxonomic terminology. Computerized "netting" analysis (clades that are nested within one another) has also been used very successfully to resolve lineages.Valich 14:11, 11 April 2007 (UTC)

I do not think "clade" should be sunk into this particular article. Although the term came to widespread use in the context of cladistics (in the strictest sense), it is almost universally employed by phylogeneticists, regardless of their attitude towards cladistics as a systematic ideology.

216.31.89.132 19:46, 17 February 2007 (UTC)

There have been changes in relationships shown in two cladograms near the top of this article.

Currently the Hymenoptera -ants, bees, wasps are viewed because of molecular data as an older early branch, while beetles are placed nearer Flies and Butterflies Diptera and Lepidoptera.

In vascular green plants Lycopods and club mosses branch first, while horsetails Equisetales and quillworts are more nearly related to ferns, but intercalary growth gives them different morphology. You may wish to update the two cladograms near the top of the otherwise excellent article.

John B. Barrett.   134.39.10.27 03:04, 8 February 2007 (UTC)

Recent molecular data indicate changes are needed in the two cladistic diagrams presented near the top of the cladistics article above. Ants and the Hymenoptera ant-bee-wasp group (order) are an older basal branch than beetles (order Coleoptera), which are nested nearer Flies (Diptera) and moths-butterflies (Lepidoptera), In the diagram of vascular green plants the basal branch should show the CLUB MOSSES (Lycopods and Selaginella), but the Equisitales horsetails and Quillworts are now placed as nested within the Ferns, including leafless Psilotum and the grape-ferns Botrychium and Oophioglossum. These cladograms should be revised. —Preceding unsigned comment added by BiologyForksWA (talk • contribs) 9 Feb 2007

Should I add old world and new world vultures as examples of convergent evolution? They both evolved similarities for eating(bald heads) but new world vultures are classified with storks now.Meson man 00:18, 29 March 2007 (UTC)

No, this is the cladistics article, and cladistics does not deal with convergent evolution in particular. Multiple examples of what are not monophyletic clades serves no purpose. If there is an aricle on convergent evolution, it might be appropriate there. KP Botany 04:07, 29 March 2007 (UTC)

Are you sure? I think the wing example is pretty obvious, but the vulture is not so, showing that we can't just base evolutionary lines on morphological evidence(even as close as the heads of old and new world vultures).Meson man 00:25, 30 March 2007 (UTC)

There are thousands of examples that are related to this, examples of convergent evolution that show this very same thing, and billions of examples of what cladistics is not. This article is about what cladistics IS. Again, the place for examples of convergent evolution is an article about convergent evolution not an article about cladistics. I love vultures, both Old and New World, and think their pictures belong everywhere. I never get bored seeing vultures in the wild, hearing them bark like dogs as their little groups warm themselves out of the trees at dawn, but that doesn't mean this article needs more examples of what cladistics is not. Maybe if you pasted a quote here, showing exactly how you would change the article, and explaining how your addition of more non-cladistical things helps the article, I would understand. Still, I urge you to consider whether this is the place for this information. KP Botany 02:20, 30 March 2007 (UTC)

LOl! they already have vultures on the convergent evolution page! I guess that's that.Meson man 03:15, 30 March 2007 (UTC)

Well, you're not the only one who thinks they're spectacular birds. KP Botany 03:47, 30 March 2007 (UTC)

That's for sure,I definently love them.Meson man 03:56, 30 March 2007 (UTC)

I am not familiar with Luria et al., but cladistics (phylogenetic systematics) was founded by Hennig. Hennig based cladististics, not on "morphological similarity," but on morphological dissimilarity. Therefore the intro is somewhat misleading. Hennig called these morphological traits, "apomorphic characters." Cladograms were originally based solely on descents based on "apomorphy" (derived morphological traits). Today, however, cladistics is not only based on morphology, but also includes weighted values of physiological, behavioral, and biochemical data; DNA-sequences, and "weighted" computer analyses to show the different hypotheses of evolutionary trait relationships, or as Hennig called them, "apomorphic characters."Valich 05:59, 8 April 2007 (UTC)

Hello Don. It's not clear that you are disagreeing with the first sentence. I think that the reference to 'order of branching' is maybe the simplest way of summarizing what you've said. Even the DNA sequences presumably fall under that same description, since by analogy we might consider those changes to be 'apomorphies of DNA.' I assume it is generally understood that Hennig did not use the term 'cladistics' for his method; that term was coined by Ernst Mayr to describe the Hennig school.

By the way, I like your recent change to the Clade article. I was hoping to eventually add the fact that Hennig cites Lucien Cuénot as the inventor of the term. My opinion is that Clade does not really need to be merged into this article since the idea predates Hennig. Someone who had a great deal of patience might even find a pre-Cuénot origin for the concept, if not the word. EdJohnston 06:23, 8 April 2007 (UTC)

Phylogenetic taxonomy was recently redirected to the section Cladistic classification. I'm a little confused by this, because I've seen people chastised on the DML and elsewhere for confusing Cladistics (the method) and Phylo taxonomy (the type of classification derived from using cladistic methods to build a tree). Is this wrong, or should PT actually redirect to Phylogenetics? I've never even heard the term "cladistic classification" before... almost seems like a contradiction in terms. Dinoguy2 14:27, 28 April 2007 (UTC)

I agree that the identity is not obvious. A change like this one ought to be sourced. Among different authors, terminology seems to vary widely. EdJohnston 15:43, 28 April 2007 (UTC)

No, phylogenetics systematics is what phylogenetics is. Phylogenetic taxonomy deals only with the area of phylogenetic systematics that is about the equivalent of cladistics, classifying organisms according to their evolutionary relationships, although it doesn't have to wind up with a cladogram. However, I will gather a couple of textbooks and post some definitions with references. But, no, PT should not redirect to Phylogenetics, only PS should, as Phylogenetics is the broad field, and PT is a subfield. KP Botany 18:50, 28 April 2007 (UTC)

'Phylogenetic' meant something different for Ernst Mayr than it did for Willi Hennig, since Mayr felt that Hennig's idea of phylogeny was bogus. I doubt that any of these two-word combinations have any meaning that is the same across all the major authors. That might suggest that any redirects will take some sourcing to justify, if they are possible at all. (Otherwise the redirect itself will not be neutral). Textbooks are OK if they are well-researched against the ultimate sources. EdJohnston 21:06, 28 April 2007 (UTC)

But did Mayr deal with this past his comments when cladistics was so new? He has books written in the last decade or so, what does he say about cladistics in these last writings? Textbooks, imo, are never well researched, for the level of detail required to discern these differences precisely in the presence of the Hennig/Mayr debate on classification. However, attitudes have changed over the years and cladistics is mainstream compared to the 30 years ago. KP Botany 23:54, 28 April 2007 (UTC)

Can you offer a generally-accepted modern definition of what cladistics is? Believed by at least two different authors, one of whom is not a cladist? (Sorry, I know I'm being difficult.. :-) EdJohnston 00:41, 29 April 2007 (UTC)

Yes, you are being rather difficult, after all this is one of the most straight-forward and easy to understand (even for the fourth grade layman) topics in modern evolutionary biology.... Hmmmm, yes, let me see what I can find along these lines, so we can attempt to put the issue, if not to rest, to nap. I think this would be an excellent and useful addition to the various articles: multiple, independent sources from non-cladists. I would like to find one from a general evolutionist, maybe see what the Japanese-American textbook author (F...) has to say, or one of the major paleontologists, and then my botanical phylogenetics texts. KP Botany 01:51, 29 April 2007 (UTC)

I am not a biologist, and found a lot of this article quite easy to understand, the cladistic method appears to be both straightforward and natural. There were some parts where I felt that either something was logically inconsistent or lacking in enough information:

Third paragraph

"A natural group" and "other forms" are not obviously technical terms and if they are, are not well defined. If "natural group" is technical, perhaps it should be in bold (as others are).

definition of basal

A species or clade is basal to another clade if it holds more plesiomorphic characters than that other clade.

For example, when considering birds and mammals together, neither is basal to the other: both have many derived characters.

I assume from this that it is difficult to enumerate plesiomorphic characters and so a comparison is not meaningful. This would make sense, but the paragraph as stands is inconsistent, both having many plesiomorphic characters does not preclude being basal, if one has more than the other.

Cladistic methods

An outgroup is an organism that is considered not to be part of the group in question, but is closely related to the group.

I would assume that a group is a set of organisms, possibly but not definitely only one, as suggested. If this is different in cladistics, it should probably be mentioned.

Clades ideally have many "agreeing" synapomorphies.

Is that between clades, or members of the clade? If it's between clades, why is this ideal?

Are these actually obvious? If not, I will try to find some other sources and update as necessary.

BananaFiend 11:19, 30 August 2007 (UTC)

1) The article should have an explicit definition of Cladogram, and a some notes about the most common styles of cladograms. Someday, cladogram may have its own Wikipedia entry, but today it redirects to Cladistics. So an explicit paragraph is warranted.

2) The article should describe the important role of software in generating cladograms. It is safe to say that the important examples of evolutionary trees we have would not exist if not for computer programs. Perhaps mention the non-deterministic nature of the programs, and include a couple of references to well-known examples.

3) Some mention could be made of the uses of Cladistics for non-lifeform applications. Although Cladistics originated in the study of lifeforms, and 99.9% of all uses of Cladistics relates to organizing lifeforms, Cladistics can be applied to other situations where a large number of objects need to be organized in a hierarchical fashion (styles of architecture, books, vehicles, styles of jazz, whatever). Even if such uses are rare or inappropriate, this article could at least mention the possibility and discuss why they are inappropriate.

Noleander 17:17, 5 November 2007 (UTC)

This might have been news to Carolus Linnaeus, since cladistics was named almost 200 years after his death. My point is that terms like 'Linnaean' and 'cladistics' are sometimes used so loosely as to create the risk of talking nonsense. The variety of approaches to taxonomy listed by Ernst Mayr in his historical books create doubt that there is one single thing called Linnaean taxonomy. Cladistics itself is far from simple (just try reading Hennig). For Wikipedia editors, following the cited sources closely is the best hope for staying grounded in a confusing area. EdJohnston 19:50, 12 November 2007 (UTC)

If you are refering to the sentence

Linnaean taxonomy insists that groups reflect phylogenies and often makes use of cladistic techniques, but allows both monophyletic and paraphyletic groups as taxa.

I did not write that ... it was in the article before I began my recent editing efforts. Most of my recent edits have been aimed at preserving the original text, which I assume is top-quality since the article was a Featured Article. If you have a suggested re-wording of that sentence, or suggest it should be deleted, let me know and I'll help out while Im in this article. Noleander 15:56, 13 November 2007 (UTC)

... and, FWIW, I think the author of that sentence (as evidenced by the subsequent sentences) was trying to say that even non-cladists use cladistic principles when organizing organisms at the Genus level (that is, non-cladists generally require that Genus' be monophyletic). The author may have intended to insinuate that the non-cladists should/could also adhere to that principle at higher levels (Family, Order, etc) Noleander 17:38, 13 November 2007 (UTC)

... I was in there editing, so I went ahead and re-worded that sentence (and the one following) to remove that phrase you mention. I also cleaned up the wording to be clearer. Noleander 18:53, 13 November 2007 (UTC)

Noleander, thanks for your reply, and your efforts to make the article better. Though Cladistics was made a featured article back in 2004, you can tell from the 'Article Milestones' box at the top of this page that it was found wanting in a more recent review in January, 2007.

'Factual accuracy' was one of his issues people complained about in that review. I worry that many people have a picture of cladistics that they construct using common sense but one which is impossible to find citations for in the actual literature. Actual cladists (and their opponents) don't always speak with 100% clarity, so it is non-trivial to get all statements correct in a Wikipedia article. The original article that became a Featured Article in 2004 had no Reference section and no inline citations, just some external links, so I wouldn't rely on it to be high quality. EdJohnston 19:20, 13 November 2007 (UTC)

There is a section in this article entitled "Preference for Monophyletic Groups" (near the bottom). The text is:

Following Hennig, cladists argue that ..... Going further, some cladists argue that ranks ..... Other evolutionary systematists argue that all taxa are .... the former which themselves were already quite advanced.

This text has been in the article awhile. Personally, I find it a bit hard to read, and it sounds like an essay or lecture, not an encyclopedia. Most of the points seem to be made elsewhere in the article. There are no citations. I wouldnt mind finding some citations, but again, most of the text is redundant with other sections in the article.

Does anyone object to the removal of this section? Or maybe pick 2 or 3 points that strike you as worth preserving? Noleander 17:29, 14 November 2007 (UTC)

I wouldn't object to removing the section Cladistics#Preference for Monophyletic Groups. An editor might restore it later if references can be found. Some of that material has been in the article for two years or more, so it would be hard to figure out who added it in the first place. EdJohnston 18:04, 14 November 2007 (UTC)

I went ahead and made that change: I preserved 3 key points in that section, but moved them into other, existing sections that were more relevant.Noleander 21:35, 15 November 2007 (UTC)

The Linnaean/Cladistic distinction seems much clearer with a detailed example. The one with which I'm most familiar, and which seems well-sourced, suitable to a lay audience, and the one experts have at the back of their minds, is the cladistic taxonomy of tetrapoda, particularly the critique of Reptilia, as detailed at Reptilia#History of classification.

I've taken a shot at writing up this example in the context of this article as per this diff; how does it look?

Nbarth (email) (talk) 01:02, 8 March 2008 (UTC)

The thing is really bad and misleading here, it should go to Phylogenetic taxonomy. Cladistics is a methodology, not a taxonomy. There are scores and scores of papers (see for example anything cutting-edge by Engel & Grimaldi on entomology) that use cladistic analysis and Linnean (or rather: evolutionary) taxonomy.

(The difference is that Linnean taxonomy is the pre-Darwin application, and evolutionary taxonomy is the post-Darwin application of the same system. Evolutionary taxonomy is basically Linne's system attempting to be monophyletic).

The pairs of opposites are:

• Cladistics vs. phenetics
• Phylogenetic taxonomy vs Linnean taxonomy

It's being confused often enough. To say "Cladistics vs Linnean taxonomy" is as if you said "Progressive stamping vs broadswords". Both are topics from the field of metalworking, but a direct comparison makes no sense.

(It is actually easier to apply cladistic methods in Linnean taxonomy, juding from how often it's being done, than to make a broadsword by progressive stamping sheetmetal. And if you read 1960s-era taxon monographies, you'll note that phenetics was used for evolutionary classification too - a thoroughly misguided attempt than nobody would half believe today and that yielded really ludicrous results, but evolutionary it was nonetheless... Adolf Engler attempted an evolutionary classification of all known plants as early as 1887, long before anyone even though of phenetics. Go figure.) Dysmorodrepanis (talk) 12:48, 11 May 2008 (UTC)

To wrap up the whole argument, see here. It is both a rigorous application of cladistics, and a rigorous application of the ICZN (the rules of Linnean taxonomy). About 70-80% of taxonomic publications these days are like that. Dysmorodrepanis (talk) 10:46, 13 May 2008 (UTC)

As an anti-example by a "taxonomist" riling against "cladists", see here. Anyone who says "phenetic cladistics" comes terribly close to utter gormlessness, if you forgive me for being so blunt. But it is interesting that on both sides of the spectrum there are people who show the same kind of misunderstanding, either by claiming "only cladistics is taxonomy" or "cladistics is bad taxonomy". Nonsense. Cladistics is the #1 tool of taxonomy, no matter what taxonomic system one follows. Every good taxonomist, Linnean or otherwise, likes and uses cladistic analyses these days.

For a more balanced critique of over-reliance on cladistics as a taxonomic tool, see here; it is a source that might be useful for this Wikipedia article, but it might be read with caution because it's perhaps a bit too opinionated still.

Whereas this would seem to be very important in the scope of this article. I have not read it, but Taxon is generally a very "Linnean" journal. According to the article's comparison table, such an paper (if it says what I think it says) should not exist. Yet it does. And from the taxonomy papers I read, it is actually quite mainstream. Or see here:

In contemporary systematics, there is a broad (but not unanimous) consensus that the hierarchy of taxonomic classification should be congruent with that of the phylogenetic tree, i.e., each taxon should constitute a monophyletic group, and paraphyletic taxa should be avoided (e.g., Ebach et al. 2006; Williams et al. 2007). Thus, although old vernacular names such as invertebrates, reptiles and turbellarians, are still in frequent use, few specialists today accept Invertebrata [excluding Vertebrata], Reptilia [excluding Aves and Mammalia] or Turbellaria [excluding the parasitic flatworms (Trematoda, Monogenea and Cestoda)] (Tyler et al. 2006) as formal taxonomic names. Moreover, no biologist would refer to Animalia as a taxon for all animals without man.

Note that their argument is strictly Linnean/ICZN:

Morphological and molecular characters support that the former clitellate family Naididae Ehrenberg, 1828 is nested within another family, Tubificidae Vejdovský, 1876. To avoid paraphyly of the latter, it has been suggested that the two should be regarded as a single taxon.

Regarding the taxonomy debate, there are a few people who advocate a middle ground like in doi:10.1080/10635150600981596, but this either is a very small minority or they're in utter CYA mode because as can be seen, the debate can get acrimonious in the extreme. Grown adults are resorting to slandering to POV-push in a relatively obscure (to the general public, and even to many "practical" and "in vitro" biologists) and highly philosophical debate. (This makes it hard to maintain NPOV, because the debate itself sorely lacks NPOV) Dysmorodrepanis (talk) 22:37, 13 May 2008 (UTC)

doi:10.1071/SB04024 is another interesting take that can be contrasted with the aforementioned synthesis. That is more in favor of the PhyloCode than of the ICZ/BN, whereas this paper has it the other way around. I'd say anyone interested in the dispute should read these two first and foremost. Because most of the papers that are published on the dispute are simply opinionated pamphlets and/or pure thought experiments unconcerned with actual organisms. Dysmorodrepanis (talk) 22:51, 13 May 2008 (UTC)

Section Cladistics#Simplified step by step procedure is a how-to, and I've tagged it as such.

How to perform a cladistic analysis is useful, and should be retained, but at Wikibooks. Some overview of the steps might be useful. So I suggest:

• Move to Wikibooks

(where it can be detailed and expanded ad libitum)

• Link to Wikibooks
• Write some overview of the steps, if it proves useful and suitable

Nbarth (email) (talk) 01:12, 8 March 2008 (UTC)

As evidenced by the size of the article and the number of related articles and references, this is a big subject, hence the main article should be a summary with links to detailed sections. I suggest that the article be broken up into sections, with summary on the main page, as per:

• Wikipedia:Summary style
• Wikipedia:Article series

Nbarth (email) (talk) 01:18, 8 March 2008 (UTC)

See above, the entire "Cladistic vs Linnean" stuff really does not belong here. Dysmorodrepanis (talk) 12:50, 11 May 2008 (UTC)

I am in the middle of deleting improperly set hyphens. Some person or persons has weird, idiosyncratic notions of when to use hyphens, that nobody else uses. Examples: "create new level-names", "arbitrarily-deep trees", "considered cutting-edge at its time". Taken together with very subtle antiidiomatic usages like "AT its time" in place of the idiomatic "IN its time", these bad hyphenations suggest editing by a nonnative speaker. In English spelling, there are many areas where opinion differs on whether to hyphenate, but this article has many examples that fall *outside* those controversies and are plain wrong. Back to setting them right. Hurmata (talk) 00:21, 12 May 2008 (UTC)

This is not a big item, but I wonder if WP:MOS really supports these changes. I'll continue on your Talk. EdJohnston (talk) 01:57, 12 May 2008 (UTC)

I think it would be as a rule ill advised to split a criticism between an article talk page and a personal talk page, and I think that holds in this case. All in the one venue or the other. To address another point, while I am ready to discuss hyphenation with people who have different views than mine, when a person doesn't have a beginning grasp of this particular subject, I'd prefer they study up on it before summoning me to debate. I don't want to spend time thinking up examples to demonstrate obvious points -- points that for most people are NOT controversial, DON'T need demonstration -- because someone couldn't think up their own examples. There are a zillion published guides to punctuation. Hurmata (talk) 05:55, 12 May 2008 (UTC)

Turning to the *genuine* hyphenation controversies I've alluded to, yes, WP:MOS addresses some of them. By reading it, one can see that my side on some of these issues is explicitly presented. So if somebody is going to let us know about WP:MOS, let them consult it themselves. "If WP:MOS really supports these changes" -- you should have said, "some of these changes". Besides, it may be a stretch to suggest that WP:MOS *supports* any stance. And *support* can be an imprecise term. Hurmata (talk) 06:30, 12 May 2008 (UTC)

Consist (talk · contribs · deleted contribs · logs · filter log · block user · block log) has repeatedly added a disclaimer to the introduction that does little beyond pointing the reader to other writer's work. IMHO, this is absolutely inappropriate for the introduction. A brief summary of the arguments may be appropriate in a Criticisms section, but why should this disclaimer be in the intro? What does it really add to the article? —C.Fred (talk) 00:33, 27 June 2008 (UTC)

Again, this text went in without discussion:

A comment: It ought to be cautioned that cladistics is a way of "looking at reality", that is, an -ism, and that the explanations below is the teachings of this -ism (cladism). For a scientific view on this -ism, the interested reader has to consult Ashlock's writings^[1], Mayr^[2], Williams ^[3] and Envall^[4]. All -isms have two faces: one for those within and one for those outside. Envall does, however, falsify cladism’s fundamental denial of paraphyletic groups empirically. It means that this part of cladism is wrong.

First, this went in the intro. I could maybe see a criticisms section, but this kind of disclaimer does not belong in the intro.

Second, Consist has alleged that he is Mats Envall. While the Journal of the Linnean Society probably passes muster as a reliable source, this hits somewhat close to original research, it seems. It certainly isn't written from neutral point of view. —C.Fred (talk) 00:15, 28 June 2008 (UTC)

Wikipedia is not a soapbox. We need to reflect what mainstream published sources have to say. Ashlock is not the only writer who has offered opinions about cladistics. Mats Envall is not the world's authority on the credibility of cladistics: Envall does, however, falsify cladism’s fundamental denial of paraphyletic groups empirically. It means that this part of cladism is wrong. User:Consist should try to find mainstream published sources that agree with Mats Envall. (He may be a lone voice in the wilderness, for all we know). EdJohnston (talk) 00:25, 28 June 2008 (UTC)

The proposed "Envall does, however, falsify cladism’s fundamental denial of paraphyletic groups empirically" makes no sense. How is one supposed to falsify a denial of a conceptual construct through empiric means? At any rate, cladistics does not "deny" paraphyletic groups; practitioners just don't use them. J. Spencer (talk) 03:31, 1 July 2008 (UTC)

Thanks for your acknowledgement of a fact, Ed. Spencer obviously does not understand Envall's point. The falsification of the distinction refers to that it rests on an empirically erroneous equalization of space and time. It may be surprising for a cladist, but it is not the less a fact, as Ed concludes. I can inform Spencer that the reason there is a fact that falsifies Hennig's confusion of pattern and process is that pattern and process are two different things. Cladists just cannot keep them apart. Einstein could. Maybe cladists should go back to school? Sorry, Spencer.Consist (talk) 07:16, 1 July 2008 (UTC)

I assume it means that Envall's point is accepted for inclusion as a disclaimer in the definition of cladistics. I thus hope that Wikipedia's editors will help to protect this disclaimer in the Criticism section. Cladists will no doubt be eager to remove it. Consist (talk) 07:19, 1 July 2008 (UTC)

See - there it was gone.83.254.23.159 (talk) 08:56, 1 July 2008 (UTC)

Cladists do not even allow a publicly known fact to be written in the criticism section. Are there any sensible persons around? Do I make myself guilty of vandalism if I put it in again?83.254.23.159 (talk) 08:57, 1 July 2008 (UTC)

EdJohnston quoted C.Fred who quoted an edit by Consist in the article. Also, the three-revert rule applies whether you adit as a logged-in user or as an anynomous user.Sjö (talk) 09:05, 1 July 2008 (UTC)

Did he? Well it looked perfectly sensible to me. Didn't it to you?83.254.23.159 (talk) 09:11, 1 July 2008 (UTC)

Does the three-revert rule also apply for those that remove facts from Wikipedia? The denial of paraphyletic groups is also a denial of the relativity of time, that is, a fact, and with it science. Don't you think it confuses students if you remove this conclusion? The denial does also deny what they study in school. Isn't there a risk that they use Wikipedia as support for a denial to learn maths, physics, chemistry and so on? Why should they learn it if facts are wrong?Consist (talk) 09:21, 1 July 2008 (UTC)

Concerning EdJohnston's comment above where he acknowledges the falsification, I can also add that I'm trying to civilize the "wilderness". The success of this civiliztion does of course depend on the strength of the civilization in relation to the grip of the wilderness. America had good use of sheriff's to civilize its wilderness. We'll see how it develops at this "open" forum (which obviously blocks facts, but approves of beliefs).83.254.23.159 (talk) 10:41, 1 July 2008 (UTC)

By the way, why is 'scientific view' put in citation marks in the title above? Doesn't science acknowledge single things and facts, which cladistics on the contrary denies, as I comprehend the situation? I see no reason to put the concept of the view within citation marks. Do anyone?Consist (talk) 10:57, 1 July 2008 (UTC)

Hennig actually confused a conceptual orthogonality (i.e., pattern and process) that is used to discuss a real orthogonality (i.e., the phenomena the concepts denote) consistently. It, of course, only means that he confuses the concepts. The real phenomena is outside of his reach. We can only choose between being consistent or inconsistent. Hennig choosed to be consistently inconsistent. It does not agree with facts, that is, is falsified by facts.Consist (talk) 11:08, 1 July 2008 (UTC)

Hennig's reasoning is actually analogous to a multi-dimensional analysis: it moves from the geometric space into the parameter space, but it does not move back again as in such an analysis, but instead stays in the parameter space comprehending this space as the "natural" space. Now, noone can deny Hennig his comprehension that this space is more "natural" than the geometric space, but it is of course wrong. The geometric space, containing for example nature, is the most "natural" thing per definition. Consist (talk) 11:40, 1 July 2008 (UTC)

Thanks for the correction of Envall's point in the article. However, "claims" is wrong. Cladistics does no doubt equalize time and space, since neither of its things, i.e., single line segments, can be differentiated with regard to time and space, which clearly is empirically wrong, since time is relative (i.e., varies with speed in space). Is it difficult to understand? Try reading the different reasonings of the Greeks Parmenides and Heracleitos. Cladistics (cladism) holds both their opinions at the same time, although they are incompatible. (That's the reason for its numerous paradoxes that C.Fred mentioned in the beginning of this discussion. One finds oneself with a lot of paradoxes if one is inconsistent, that is, self-contradictory. The way out of the paradoxes is to use concepts consistently, but then reality is, on the other hand, ambiguous. The choice is thus between paradoxes and ambiguity. Just choose. Unambiguity and unparadoxicality is not among the choices). —Preceding unsigned comment added by Consist (talk • contribs) 13:07, 1 July 2008 Consist (talk) 13:10, 1 July 2008 (UTC)(UTC)

Thanks again for the inclusion of empirically. However, since you use the word "claims", I would like to know which criterion Wikipedia uses for a decision of when an empirical falsification turns from a claim of a falsification into a falsification? Because in science there are no such criterion - falsified is simply falsified. It is an important issue, since although you may use the concept claim together with the concept falsification, like in claims to have falsified, the concept claim is actually on the same level as the concept falsify, but there is a huge difference between them. Cladistics, for example, claims that only holophyletic groups (erroneously called monophyletic groups) are natural groups without any definition on the concept natural groups. Anyone can thus claim anything (abstract or concrete, right or wrong). A falsification, however, marks the boundary between right or wrong, actually the only common criterion we have to distinguish right from wrong. I have thus falsified cladism's denial of paraphyletic groups empirically, not claim to have falsified it. You must not make truth and lies into a matter of fifty billion flies can't be wrong, because history has over and over again shown that they not only can, but moreover most often are. Facts, however, like the relativity of time, is not and will never be wrong. We simply grow older in slower pace the higher speed we travel with. We do and we will always do.83.254.23.159 (talk) 15:19, 1 July 2008 (UTC)

I have restored "claims to" as it is perfectly accurate. That you say that you have falsified something doesn't make it so. I suggest that you wait until your paper has been discussed and accepted by the scientific community. Until then, this article can not state as undisputed fact that you have falsified any aspect of cladistics. Please se WP:UNDUE. Your falsification, like all of science, is tested by scientists, not by Wikipedia editors. When those tests lead to your arguments being accepted, then they will be included in the article. I suggest that you focus your efforts on making your paper known and accepted among scientists before you continue the discussion here.Sjö (talk) 05:06, 3 July 2008 (UTC)

Sjö obviously do not understand science. Cladistics (more correctly cladism)confuses time and space in its sole recognition of holophyletic groups (i.e., denial of paraphyletic groups), defined as "an ancestor and and all its descendants"; a confusion that can be expressed as Time=Space. This definition leaves no possibility for time to be relative to space, which it obviously is. Now, this doesn't mean that cladism's definition falsifies the relativity of time, but that relativity of time falsifies cladism's distinction "holo- and paraphyletic groups", and thus also, of course, its "denial" of paraphyletic groups. This will never change independently of how many people that accepts it. Cladism's distinction (and denial) will be inconsistent, self-contradictory and empirically wrong forever and ever. The relation cladists fail to recognize is that holo- and paraphyletic groups are orthogonalities within monophyletic groups. This is what Envall explains in his paper (in addition to the falsification of the denial of paraphyletic groups itself). The falsification is thus not a claim, but a fact. It doesn't change in relation to how many people that accept it. This fact means that cladism denies both facts and science. Consist83.254.23.159 (talk) 15:53, 3 July 2008 (UTC)

(indent reset) If these facts are so abundant, then there should be multiple, readily-available sources to demonstrate them - and explain them in straightforward English. —C.Fred (talk) 16:15, 1 July 2008 (UTC)

See above.

What in the world is a "denial" of paraphyletic groups? Practitioners of cladistics don't "deny" them, they just recognize that Prosauropoda or Thecodontia or [insert paraphyletic group of choice] as traditionally defined do not include all descendants, and they avoid using such groups. I'm going to chalk it up to English not being your first language, but your writing style is not lending itself to understanding. You are simply not making sense, and appear to be trying to solve a problem that doesn't exist (or if it does, makes no practical difference).

The first question has to be put to a cladist. As far as I understand, it means that cladists do not accept paraphyletic groups, although they are monophyletic groups. The problem Envall addresses is that cladists point at holophyletic groups calling them monophyletic groups as if paraphyletic groups are not monophyletic groups. He explains that such a confusion of holo- and monophyletic groups actually is a confusion of one specific with its generic, leaving the other specific of the same generic outside, and that it is inconsistent, self-contradictory and wrong. This is important to understand, since being wrong leads the thought astray. One simply gets lost. However, in your last two statements (within the parentheses) you appear to be insecure about whether there is a problem or not, but none the less seem secure that it makes no practical difference. It would be interesting to find out how you arrive to a conclusion that a problem you don't know whether it exists or not makes no practical difference. I, on the contrary, am sure that an inconsistent, self-contradictory and empirically erroneous comprehension makes a h-ll of a practical difference from a consistent comprehension. The former is actually practically useless. Consist83.254.23.159 (talk) 15:53, 3 July 2008 (UTC)

Now, to other matters. There are nine papers cited in the criticism section. Six of them were written before 1980, and seven of them have either Ashlock or Mayr as authors; these include the six pre-1980 papers. The section then goes on to feature a statement that, as far as I can tell, boils down not to a criticism, but to a difference. "Falsified cladistics' denial of paraphyletic groups empirically" is meaningless in English; the most I can get out of it is that denial of paraphyletic groups is somehow a bad thing, although it is not explained how "cladists" "deny" paraphyletic groups, nor why this *should* be a bad thing. All I get is that "cladists" deny them, and I have no idea what that is supposed to mean or why it is important. The net effect of the section is confusion. Frankly, it makes criticism of cladistics look bad. To cite nine papers, but to have only three of them written after the field took off, only two of them in the last decade, and seven of them by the same two people, it makes it look like criticism is a thing of the past and on the fringe today. To then add a specific criticism that doesn't make sense, does not help. Are there any legitimate, straightforward, readable criticisms of cladistics that do not boil down to matters of philosophy or "I don't like that I'm not supposed to use Thecodontia [or whatever] anymore?"

The criticism is that the distinction of holo- and paraphyletic groups calling holophyletic groups monophyletic groups is an inconsistent, self-contradictory and empirically erroneous confusion of pattern and process. It is simply both a conceptual confusion and an empirical error at the same time. This criticism is not a matter of philosophy at all, but of the cladistic conceptual confusion not agreeing with facts. The consistent conceptualization of phylogenies is instead a system of the Linnean kind, that is, using categories of categories. These statements are simply facts, not claims. Consist 83.254.23.159 (talk) 15:53, 3 July 2008 (UTC)

Actually, there are areas where there has been debate, even recently. I'm thinking of topics such as how to code information, how to weight characters, choice of taxa to include, the effects of missing information, should taxa be compartmentalized based on a-priori work, et cetera. There are much more meaty ways of going at a criticism of cladistics than abstract, philosophy-of-science concerns or knee-jerk resistance from the old guard.

I guess the bottom line, Consist, is this: As the man said, "whatever gets you through the night, 'salright," but this article is something else, and what you are doing at this article is not in fact helping others understand the topic or salient criticisms of the topic. J. Spencer (talk) 03:06, 2 July 2008 (UTC)

Now you're talking! You're mentioning the word 'fact'. You're saying that what I do is not in fact helping others to understand that topic. Where did you get this "fact"? From your own head? Well, Envall is, on the contrary, of the opinion that the cladistic denial of the relativity of time and science is in fact not helping others to understand neither reality (including evolution) nor science, but, on the contrary, confuses their possibilities to understand both. It is an inconsistent, self-contradictory and empirically erroneous model that confuses pattern and process. Consist (talk) 18:17, 3 July 2008 (UTC)

The criticism section might be WP:UNDUE since it's not remarcable or unusual that a field of science is tested or criticised. Right now, the only person mentioned is Envall, who compared to e.g. Mayr is a minor player with a paper that has only been discussed on one English and one Swedish blog. If there is criticism section I think that Mayr's view should be included, as the more prominent scientist.Sjö (talk) 19:22, 2 July 2008 (UTC)

I guess the minor player Envall has nothing against including neither Mayr's nor Ashlock's point. It is the same point as Envall's, if not expressed as concentrated as Envall's true statement that the cladistic distinction of holo- and paraphyletic groups erroneously calling the former 'monophyletic groups', and subsequent denial of paraphyletic groups is an inconsistent, self-contradictory and empirically erroneous confusion of pattern and process. Ashlock called cladism a paranioa, which is exactly what Envall does with the statement above, and which also is exactly what it is according to the definition of paranoia. Interestingly, cladists call their mental antagagonist 'para'-phyletic groups. Noone had even heard about them before Hennig wanted to get rid of them, and no cladist has succeeded to define them till this day, although Farris tried. I can, however, define them: they are the left-overs of Hennig's bold confusion of pattern and process. It is easier for me to see what they are, since I see the confusion. Both Mayr, Ashlock and Envall defend science against this confusion. The consistent conceptualization of phylogenies is a system of the Linnean kind, that is, categories of categories. It does not contradict facts, because it keeps the orthogonal pattern and process apart consistently. Consist (talk) 18:17, 3 July 2008 (UTC)

If there is someone that doesn't understand it, I have to clarify a fact. If one's comprehension doesn't agree with facts, then one is wrong. There's no way out of this fact. Cladism is wrong in confusing pattern and process, that is, space and time, because it erroneously denies the fact that time is relative to space. An illustration of a phylogeny is a process-model, not a pattern, and a consistent comprehension of it in terms of pattern and process is that the external line segments represent single pieces of pattern, whereas the internal line segments represents two pieces of pattern in a row, that is, single pieces of process. Hennig confused external line segments with internal line segments, which thus confuses single pieces of pattern with single pieces of process (i.e., thing with kind). This also equalizes time with space, which contradicts the relativity of time. Is it impossible to understand?Consist (talk) 18:50, 3 July 2008 (UTC)

Cladism conquers the world by choking its opponents, including the moderate phylgeneticists that refuse to abandon a scientific approach for cladism's confusion. This is in line with an extremist approach. When discussing criticism of cladism, we have to bear in mind that whereas moderate phylogeneticists criticizes cladism, cladism actually denies a moderate (i.e., scientific) approach. Phylogeneticists does not deny cladism. That's why the contributor above (Spencer?) actually argue against having a criticism section using arguments like that the criticism is so bad that it makes the criticism look bad. Well, if so, why not Spencer straighten up the criticism. Spencer also makes a point of that he doesn't understand anything of it as if this point disqualifies the criticism instead of Spencer. The criticism is of course written for people that understand it. Those that don't should at least not use their inability to understand to argue against a criticism section. I instead interpret Spencer's inability to understand as the reason for his cladistic approach. To me, cladism is a belief for the narrow-minded, like all other -isms. It fits people that can only keep track of one line of reasoning at the time. Science is a matter of logic, consistency and agreement with facts. Cladism's logic error is that it uses propositional logic for a reasoning that has to use first-order (predicate) logic, since propositional logic does not even include quantifiers like every (i.e., all) or some. Cladists can learn about them in Wikipedia. Cladism's consistency error is that it first "defines" a representation of one thing (i.e., an external line segment) as one thing, and then also "defines" a representation of two things in a row (i.e., an internal line segment) as one thing. Cladism's error in agreement with facts is that it denies the proven relativity of time per definition. It means that cladism is wrong in all possible ways. Cladism is actually the contrary to right. All this makes cladism extremely difficult to criticize; in which end should you start? Ashlock choosed one end, Mayr choosed another and Williams choosed yet another. Envall choosed to focus on the worst problem, that is, its disagreement with facts. It is a problem no approach that claims to be scientific can live with. I bet Ed Johnston (above) realized this fact. Sjö is a whole-hearted cladist, whereas Spencer doesn't understand anything. Why is Spencer participating in this discussion at all?Consist (talk) 22:14, 3 July 2008 (UTC)

Don't be cute, Envall. It is you, after all, just as 83.254.23.159 is. I don't understand what you are saying because, in fact, you are not saying anything. You are just stringing together words. Is that clear? J. Spencer (talk) 00:46, 4 July 2008 (UTC)

Agree with J Spencer here. Even if there is non-poetic merit to what you are saying, it is original research and inappropriate for you to add it yourself. Moreover, your confrontational approach is counter to the wikipedia ethos, and distracts from any potential merits in your arguments. de Bivort 01:24, 4 July 2008 (UTC)

Much does one have to hear before one's ears fall off. Spencer says that I'm not saying anything, but just "stringing together words", and Debivort agrees. Isn't "stringing together words" exactly the definition of saying? What does Spencer and Debivort do when they say something if not string together words? However, my message is that cladism cross-defines things as both single things (i.e., external line segments) and two things in a row (i.e., internal line segments) thereby confusing pattern (i.e., single things) with process (i.e., two things in a row), and that this is inconsistent, self-contradictory and empirically wrong (i.e., not agreeing with reality). The reason it doesn't agree with reality is that pattern (i.e., space) is existentially distinct from process (i.e., time) as witnessed by the fact that time is relative to space. However, instead of recognizing the inconsistency, cladism "denies" it per definition, and with it also both facts, science and present. Cladism is thus an inconsistent comprehension of reality that "denies" its inconsistency, and thus also reality, with a definition. It puts the map in front of the reality the map portrays, and since a perfect projection is impossible, it is a getting lost in itself. However, instead of recognizing that it is lost, it defines that a perfect projection is possible. Cladism is thus the orthogonality to science, but whereas science is consistent, cladism is consistently inconsistent. These arguments may appear confrontational, but my aim is to convey the situation as clearly and concentrated as possible. We have to be consistent in our use of concepts to avoid getting lost among words. My message is that Hennig's conceptualization of phylogenies using a distinction of monophyletic groups into holo- and paraphyletic groups is inconsistent, self-contradictory and wrong, whereas Linnes system is consistent and correct. That's how I string together words.83.254.23.159 (talk) 07:24, 4 July 2008 (UTC)

Another question is why it should be inappropriate of a reasearcher to add original research to Wikipedia if that reasearch consists of an empirical falsification of an inconsistent conceptualization? A falsification is valid and thus a scientific truth in the moment it is demonstrated. Hennig's conceptualization of phylogenies is simply empirically erroneous, that is, wrong. I bet it came as a surprise to cladists that an inconsistent conceptualization can be falsified by facts at all, but now it is actually the case. The reason is that this particular fact is the only fact we have for the existence of reality, which the conceptualization in practice denies. I can't see why it should be inappropriate for any person to convey this fact both in scientific journals and on open encyclopedias like Wikipedia. On the contrary, I see it as a duty for a person who understands this devastating inconsistency. It would be irresponsible to allow humanity to be led into confusion without trying to stop it.83.254.23.159 (talk) 08:19, 4 July 2008 (UTC)

I can also add that the reason Hennig's conceptualization is inconsistent is that it distinguishes between the concrete and the abstract, where the abstract is a representation of the concrete. These two phenomena are, of course, indistinguishable. Cladism, however, instead "denies" the concrete. Linnes system is, on the contrary, a consistent synthesis of the concrete and the abstract. It kind of interweaves the two into a consistent whole. That's why it's so fantastic. The problem cladism addresses is that reality is conceptually ambiguous. This problem is, however, due to the existential difference between space and time, and thus something we cannot "solve". The result of Hennig's conceptual confusion is only that it transfers the ambiguity into concepts, which an encyclopedia ought to react strongly against. If not, the encyclopedia may find itself involved in an increasing number of battles about the definitions of concepts. An encyclopedia has a huge interest in keeping the aisle between concepts. There are synonyms, but no concept equals another. All concepts are instead defined by other concepts. (Does Spencer understand anything of this?)83.254.23.159 (talk) 09:13, 4 July 2008 (UTC)

Stringing together words does not equal meaning. J. Spencer (talk) 15:04, 4 July 2008 (UTC)

That's true Spencer! You got that one right. No concept equals another concept. What you meant to say is probably that stringing together words does not necessarily convey a meaning. No it doesn't. It isn't necessarily consistent or the truth either. I can also inform you that I'm not a researcher at all. I do have a degree, and have done a post-doc at the Smithsonian molecular lab, but presently I'm acting as a biological analyst. My paper in BJLS is only an establishment of a fact. I just thought it was necessary to straighten out Hennig's confusion before the whole world had gone mad. If it does despite my clarification, then be it. I did what I could. Humanity gets what it deserves. 83.254.23.159 (talk) 16:55, 4 July 2008 (UTC)

Spencer is of course welcome to discuss the issue in any scientific journal (I would suggest cladistics). Then you do have to string together words in a way that conveys a meaning, and the meaning has to explain why cladism's distinction of monophyletic groups into holo- and paraphyletic groups, and the subsequent denial of paraphyletic groups is falsified by facts. I welcome such a contribution.83.254.23.159 (talk) 17:09, 4 July 2008 (UTC)

Dear editors (or the users with more power than the rest of us), I welcome your acknowledgement of Envall's falsification. It is an even more important understanding at the present stage of biological systematics, since cladism has recently reached its ultimate erroneous conclusion (which, by the way, is the same as its erroneous initial assumption), that is, that relationship is relative instead of that time is relative (see Reif in Cladistics). I don't know if its proponents yet understand that their conclusion actually excludes that time is relative; they seem to think (believe?) that it instead excludes that relationship is absolute, but the erroneous view has at least reached its final point. Now, we just have to wait for the public decision of what that is absolute and what that is relative. Interestingly, these two conclusions (cladism's erroneous and Einstein's correct) are actually also orthogonalities (i.e., orthogonal to each other) in the eternal merry-go-round that concepts form. The difference between them is that cladism's is wrong, whereas Einstein's is right. In order to arrive to Einstein's conclusion, we have to understand that humanity preceeded concepts, but not single humans. The fact that causes the impossibility to accept both at the same time is that space cannot equal time, since it would deny process. Hennig took the erroneous step to equalize space with time (with a definition), thus definitionally denying process. Envall demonstrated that this comprehension (definition?) is wrong by denying the empirically proven fact that time is relative. It means that Linné hit the nail, independently of whether we like it or not. I may dislike it even more than cladists do, but I will never deny a fact. (Does Spencer have any stringed words to add to this reasoning?) Consist (talk) 22:06, 6 July 2008 (UTC)

The criticism section should actually have the title: Science strikes back - falsifies cladism's denial of it empirically.Consist (talk) 21:29, 7 July 2008 (UTC)

Not even the Flat Earth article has a section header that non-neutrally slanted. —C.Fred (talk) 22:32, 7 July 2008 (UTC)

As I have stated everywhere, there is no neutrality to be found between cladism and science. Cladism denies facts, whereas science acknowledges them. There's no neutrality between accepting and denying facts. Or, can C.Fred possibly find one? In my point of view, science is neutrality. Doesn't C.Fred agree with this view? Consist (talk) 23:28, 9 July 2008 (UTC) Consist (talk) 23:26, 9 July 2008 (UTC)

If you thesis is right, and there is no reconciling science and cladistics, then talking about cladistics from a science POV introduces non-neutral bias. The encyclopedia does not tolerate refutations of religion in the introductions to religious articles because they are incompatible with science. Same applies here if you are correct. In either case, your additions have been inappropriate so far. de Bivort 01:55, 10 July 2008 (UTC)

Good attempt Debivort (sorry for misspelling your name the last time), but you obviously do not see that you're wrong. This particular religion is testable and thus not incompatible with science. Its denial of paraphyletic groups equalizes time and space, and does thereby leave no possibilities for time to be relative, which it obviously is. This misconception has already led one cladist (Prof. Reif, Cladistics) to the silly conclusion that relationship is relative instead of time, which, symptomatically is the same comprehension as cladism's original assumption, since cladism is a (circular) paranoia confirming its own assumptions. The incompatibility between cladism and science lies in that cladism also denies science by its denial of paraphyletic groups. It thus does not leave any possibilities for phylogenetic science either. It so-to-say closes the zip for a sensible, correct and scientific phylogenetics. If this would be clear to all involved editors of Wikipedia, and also would protrude in Wikipedia articles, then everything would be OK. If it isn't, and doesn't, then Wikipedia actually helps to spread a confusion that also will hit Wikipedia itself in the end, since cladism consistently ambiguates concepts by confusing them. This should be clear for any sceptical observer that takes a look at the "definition" of cladistics and phylogenetics. Cladists do all they can to confuse the concepts, although cladistics' denial of paraphyletic groups is inconsistent, self-contradictory and wrong, and thus does not have anything with science what-so-ever to do. If phylogenetics is a science, like genetics, then it cannot be synonymous to cladism. On the contrary, the two are orthogonal, or contraries. However, your last sentence implies that it doesn't matter whether your arguments are right or wrong, it is actually me that is in focus, not my message. Well, concerning me, I can tell you that I will continue correcting Wikipedia for one year, two years, three years, and so on... Either from my ip-adress or from another. I will never accept a religion's denial of science, especially not when Envall has shown that the religion does not agree with facts. Why should I? Scince is right and cladism is wrong. This has Envall shown to be the truth. Those that do not accept it do voluntarily leave facts as The Criterion of being right or wrong. God knows how they will decide their disagreements.... Maybe by "prominent" authorities (like Farris and Nelson), as Sjö seemed to favor, but, whose authorities? No, cladism is out cycling as we say in Sweden. The worst thing is that I can sense a similarity in the behaviour of cladists and America in the world; both appear to believe that they can force their comprehension to become a truth. Luckily, Envall has shown that they can at least not make time non-relative, just as they can't make paraphyletic groups non-monophyletic. 83.254.23.159 (talk) 22:07, 10 July 2008 (UTC)

I just looked at how Wikipedia treats other religions, like, for example, scientology. In this article, there is a section discussing "controversies". This may be a good solution of handling the scientific controversies with cladism. The problem for science is that cladism claims to be science (a paradigm shift) and denies science as we know it (including testing statements against facts). For example, when I argued to a cladist that science can only discuss testable statements, he commented that it was the most narrow-minded perspective on science he had ever heard. This is actually the difference between cladism and science. Cladism abandons facts for a belief. Its particular belief appears sensible, and it is, but its denial of conceptualization isn't. The truth is that the difference between process and pattern (i.e., between time and space) is an ambiguity we cannot get rid of. We can only choose between placing it in reality or in our concepts. Science places it in reality, whereas cladistics (i.e., cladism) places it in concepts. Science is consistent, whereas cladistics is consistently inconsistent. This is not a criticism of cladism, but a recognition of a fact. This recognition does not belong in a criticism section, but maybe in a controversies section. The main problem with cladism is that it claims to be science instead of science, although it is incompatible with facts. It actually denies both facts and present.Consist (talk) 23:10, 10 July 2008 (UTC)

You say " I will continue correcting Wikipedia for one year, two years, three years, and so on." If your corrections fly in the face of consensus and you are as persistent as you say you will be, expect to be blocked. But this will not happen if you stay non-disruptive. Just a heads up. de Bivort 00:19, 11 July 2008 (UTC)

As I have explained before, I don't care about whether I'm being blocked or not. I'm not doing this for my own sake, like cladists are, but as a civil duty. I'm only trying to help humanity from falling into confusion. I will act the way I find necessary and gradually adapt to the way I'm treated. I'm used to solving problems. I refuse my message to be hidden under mat. This far, I have only been granted a tiny sentence erroneously put in a criticism section, and even the inclusion of this tiny sentence is questioned (among others of Sjö), although cladistics is among the largest frouds in history. Maybe, it is the size of the froud that is almost unimaginable. I spell out clearly that the foundation of cladistics, that is, the denial of paraphyletic groups (or orthogonally expressed: the sole recognition of holophyletic groups) is inconsistent, self-contradictory and (empirically) wrong (that is, not agreeing with facts). This is the reason for its innumerable paradoxes as C.Fred mentioned in the beginning of this discussion. Life is full of paradoxes if one is consistently wrong.Consist (talk) 21:58, 11 July 2008 (UTC)

(indent reset) My message is that cladism is an inconsistent, self-contradictory and emprically erroneous conceptualization of dichotomously branching processes (i.e. phylogenies), whereas the Linnean system is a consistent and correct conceptualization of such processes. It means that cladism confuses concepts in a way that contradicts itself, and also does not agree with facts. If this message "flies in the face of consensus". as Debivort expresses it, then Wikipedia has disqualified itself from being an encyclopedia as far as I understand. The characteristics of an encyclopedia, as developed from the characteristics of a dictionary, is, according to Wikipedia: The encyclopedia as we recognize it today was developed from the dictionary in the 18th century. A dictionary primarily focuses on words and their definitions, and typically provides limited information, analysis, or background for the word defined. While it may offer a definition, it may leave the reader still lacking in understanding the meaning or significance of a term, and how the term relates to a broader field of knowledge.
To address those needs, an encyclopedia treats each subject in more depth and conveys the most relevant accumulated knowledge on that subject or discipline, given the overall length of the particular work. If my message does not offer an understanding of how the term {i.e., cladistics] relates to a broader field of knowledge [i.e., science] then I must have misunderstood the expression relates to fundamentally. What's the problem? Why can't Wikipedia include the information that cladistics is an inconsistent, self-contradictory and erroneous conceptualization of dichotomously branching processes when it has been clarified in the scientific literature (properly reviewed)? You have to understand that there are lots of intelligent people out there that sense that there is something wrong with cladistics, but just can't find out what. Why not offer an understanding of how the term {i.e., cladistics] relates to a broader field of knowledge [i.e., science] Consist (talk) 21:22, 12 July 2008 (UTC)

I just included a controversies section. Will you block me now? Have I gone too far in displaying the truth?Consist (talk) 22:27, 12 July 2008 (UTC)

I seriously think the entire controversy stuff is misplaced here and it has come to the point where it is dragging what once was a good, concise and easy-to-understand article in the muck. "Cladistics" is not the opposite of Linnean taxonomy"; cladistics is an approach to resolve phylogenies. What taxonomic consequences you draw from them is another matter entirely. And if your computer is able to handle the amount of computing (which quickly grows to be gargantuan), cladistic analysis is the way you will want to use these days. There are a few cases where you have such massive amounts of data that you can only run a phenetic neighbor-joining algorithm (which scales much less drastically), but these are getting rarer and rarer as better and better computers become available. And there is as far as I can tell no significant controversy. There is dispute about the interpretations of the results of course - after all, it's just inference, that is to say: glorified statistics. But if you think otherwise, I challenge you to show me a recent peer-reviewed paper where it is succinctly argued that there is a better way to resolve phylogenies than cladistic analysis.

The controversy is not about "cladistics", it is about "cladism" - or as I prefer (because it is so much clearer) "phylogenetic nomenclature" (PN) - versus "Linnean nomenclature" (LN). I have played around a bit with both, and I can only say that both have serious flaws - one rests uopn a limited number of hierarchical levels, the other rests upon hypothesized unknowns. One cannot appropriately express the evolutionary relationships of synapsids, the other is incapable to classify prehistoric horses or Cnemidophorus species in a meaningful way. And therefore I remain unconvinced of either, noting simply that the ICZN does not touch anything above superfamilies, giving researchers free hand out there, and that is perhaps the only positive thing that can be said (though I have to kudos the ICZN for trying to keep out of the debate).

As I have said above, "cladistics" and "Linnean taxonomy" are not only not incompatible, they are actually the single most common combination of phenetics versus cladistics, and PN versus LN. You doubt that? Google for cladistic and superorder (or "superfamily" or whatnot). If the preposterous (if only because of the headers) comparison table were correct, you would receive a handful of hits that would all go along the lines of "cladistics does not use ranks such as superorders...". But instead, there are thousands of hits like "A cladistic analysis of whiteflies, subfamily Aleyrodinae". Which will of course make anyone who has strong opinions about PN or LN scream bloody blue murder, but as it seems the vast majority of researchers simply do not have any strong opinions, treat taxonomy/nomenclature as expedient, love it when their PAUP* does not crash, and often enough happily use Linnean ranks. Which if the comparison table were true could not exist. Yet it exists, and it actually thrives. I'd safely estimate that 90% of all major decisions in Linnean nomenclature rest upon a cladistic analysis in some way these days, so overwhelming is the importance of cladistic analyses. That's because for certain taxa, the (Linnean) ICZN is the only formal and widely-accepted set of rules for taxonomy; it's a case of "better the devil you know".

So take your dispute to the phylo-taxo article where the subject matter in dispute properly belongs, and take that table with you but change the headers, and slug it out there. But I will not stand to see the good name of cladistics, the approach about every serious evolutionary biologist likes to use these days for resolving phylogenies, be tarnished by controversies between proponents of PN vs LN.

If you have not done so, you should really read this. And you may be interested in this historical review of the Cronquist system, which states a point that might seem cladist, or in favor of PN - only that PN in the modern sense had been invented 4 years earlier and was all but unknown outside dinosaur paleontology; it is a critique of paraphyly from inside Linnean nomenclature. Oh, but I just read the Wikipedia article on "Cladistics" and it says that "Cladistics" and "Linnean Taxonomy" are incompatible camps which are almost at war with each other? Damn... Or consider the following quote from doi:10.1080/09670260701419921:

Rank does, of course, provide a marker for where we are in any particular arrangement, yet it is pointless to ask, what is a family or what is an order, etc.? That does not mean the groups so indicated are devoid of meaning. The kinds of groups recognized – family 1 and family 2, sub-family a and sub-family b in Fig. 3 – are monophyletic. In evolutionary terms that means the group contains all the species having the same most recent common ancestor, and there is evidence (characters) at the relevant node to support such a contention.

Must... not... exist... is... not... black-and-white... does... not... compute...

And you should do what I have done, but what few in this debate seem to have done: grab yourself a non-cladistic paper, e.g. this. You will - not at first, but soon enough - note a difference that you are simply not aware of as it seems. For I seriously wonder who of you who debate so fiercely here actually knows anything outside cladistics - that is, has ever seen a phenetically inferred phylogeny (on which they used to base "Evolutionary taxonomy", a gross misnomer if there ever was one). Because if you do, you will immediately realize that both schools of taxonomy make use of cladistic analyses as often as they can these days.

In a nutshell:

• the only remaining issue between cladistics and all other means of inferring relationships between taxa is that some old-schoolers (who perhaps personally quarreled with Hennig or whatnot) do not use it, but such people are few and far between.
• there is acrimonious, vitriolic and bordering on the plain hateful controversy between cladists - people who think that taxonomy should not only represent evolution (as has been the consensus since 100 years or so) but inferred phylogeny and that the only good taxon is an unranked clade -, and people who love their paraphyletic taxa or just want to raise a stink out of principle. But that properly belongs at Phylogenetic nomenclature.
• Most researchers - people who use taxonomy as opposed to taxonomists - simply seem to consider the controversy to be too arcane, and go on with their research, and many of them will boot up the old PC, feed it their alignments, run PAUP*, go on a vacation, and when they return they check the results and move some family from one order to another based on the cladistic analysis.

An interesting development that, if the article in the present state were correct, could impossibly exist: there is currently a movement to permit non-monophyletic taxa in the PhyloCode (discussed here, and there is currently a movement to prohibit paraphyletic taxa in the Linnean codes (see Williams & Kociolek above).

Go figure.

As a small reminder, this is a not-too-shabby representation of how the "tree" of life looks like. Dysmorodrepanis (talk) 04:47, 27 July 2008 (UTC)

I would say that a short and proper definition of cladistics is: an inconsistent, self-contradictory and empirically erroneous comprehension of dichotomously branching processes, which partly was accepted in spite of its shortcomings by a diffuse belief that it might be correct in some sense, partly was enforced on those that didn't want to participate in it, and partly was enforced by internal cooperation by those that acknowledged it. It is not, I repeat not, synonymous to phylogenetics, but rather an extremism within phylogenetics. It rests on a denial of paraphyletic groups, which is neither a necessary nor a correct component of phylogenetics. Consist (talk) 22:34, 10 July 2008 (UTC)

The problem with cladistics is that it confuses an erroneous comprehension of dichotomously branching processes (i.e., phylogenies) with techniques to reconstruct such processes ad hoc. It means that its definition of itself includes both its erroneous comprehension and existing techniques, although the two are clearly distinct. An erroneous denial of paraphyletic groups is not a necessesary prerequisite to reconstruct or discuss hypotheses about phylogenies. Phylogenies themselves are not in question, but only conceptualization of them. The problem with cladistics' erroneous conceptualization is that it leads to erroneous deductions, like, for example, that relationship is relative instead of time, whereas the advantage with a correct conceptualization is that it instead leads to correct deductions, like, for example, that time is relative. The "problem" with paraphyletic groups has to be understood in terms of things and their parts. Which monophyletic groups that are relevant for different considerations depends on which things we use for which questions. The two possibilities is that we may want to find out (1) the relationship between things or (2) more inclusive things by their parts. Now, different kinds of techniques to reconstruct phylogenies are equally useful to find answers to both of these questions, but whereas cladistics' actually excludes the latter of these questions by "denying" it, a consistent and correct comprehension like the Linnean system does not exclude any of them. It shows that a definition of cladistics ought to focus on its comprehension of phylogenies, since it is this property that distinguishes it from a scientific comprehension of phylogenies. Cladistics and science are only incompatible in their comprehension of phylogenies, nothing else. The difference between them is only that whereas cladistics comprehends internal line segments as representations of single things (i.e., pattern), science insted comprehends them as representations for two things in a row (i.e., process). This difference means that whereas cladistics is inconsistent, self-contradictory and wrong, science is consistent and correct. Science simply conceptualizes phyogenies consistently and correct. Concerning cladistics' claim of being "natural", I can only point at that science rests on the assumption that simultaneity (or concurrency) is "natural", and that it is an undeniable fact. If cladistics' is "natural", then "natural" does thus not agree with facts. Consist (talk) 23:21, 13 July 2008 (UTC)

Source all of this if you want it read. Your opinions don't an encyclopedia make. A blog, yes. An encyclopedia, no. --Blechnic (talk) 07:21, 14 July 2008 (UTC)

I don't understand what you refer to as the "source of this" - "if you want it read". I draw to the attention that Envall has falsified cladism's (cladistics') denial of paraphyletic groups empirically. It is just as any scientific study. Envall has taken cladism's hypothesis that only holophyletic groups are "natural groups" (and thus that paraphyletic groups should be denied) and tested it empirically, and has concluded that it does not agree with facts (i.e. that time is relative to space). This is a discrepancy between cladism and facts that will last forever. Exactly what is it that Blechnic think is wrong with my wish to include this fact in the definition of cladism (cladistics)? (The talk about blogs is ridiculuous). Consist —Preceding unsigned comment added by 83.254.23.36 (talk) 23:50, 26 July 2008 (UTC)

"Cladistics" can only indicate that groups are paraphyletic. "Cladism" can (and does) deny paraphyletic groups any taxonomic meaning. As long as you both will fall to the canard that "cladism" = "cladistics" rather than "cladism" = "phylogenetic nomenclature" = "strict taxonomic application of cladistics", the dispute is unresolvable. Dysmorodrepanis (talk) 11:20, 29 July 2008 (UTC)

I can add that I will return until the fact that cladistics does not agree with facts is included in the definition of it. Consist —Preceding unsigned comment added by 83.254.23.36 (talk) 23:53, 26 July 2008 (UTC)

If I may add yet another quote:

In contemporary systematics, there is a broad (but not unanimous) consensus that the hierarchy of taxonomic classification should be congruent with that of the phylogenetic tree, i.e., each taxon should constitute a monophyletic group, and paraphyletic taxa should be avoided (e.g., Ebach et al. 2006; Williams et al. 2007). Thus, although old vernacular names such as invertebrates, reptiles and turbellarians, are still in frequent use, few specialists today accept Invertebrata [excluding Vertebrata], Reptilia [excluding Aves and Mammalia] or Turbellaria [excluding the parasitic flatworms (Trematoda, Monogenea and Cestoda)] (Tyler et al. 2006) as formal taxonomic names. Moreover, no biologist would refer to Animalia as a taxon for all animals without man.

When DNA data confirmed that leeches (Hirudinea s. str.) and their close relatives, Branchiobdellida and Acanthobdella, are all derived oligochaetes (Martin 2001; Siddall et al. 2001), the traditional classification of Clitellata into two major taxa of the same rank—Oligochaeta and Hirudinea—was no longer appropriate; thus, the names Clitellata and Oligochaeta are synonymous. In this case, use of these two names becomes optional—they refer to a rank above the familygroup level for which no priority rule applies. For family-group names, and names of lower rank, however, priority does apply; see Article 1.2.2, International Code of Zoological Nomenclature [the Code] (International Commission on Zoological Nomenclature [ICZN, the Commission] 1999).

It is from Zootaxa 1744: 66–68, titled: "ICZN rules – a farewell to Tubificidae (Annelida, Clitellata)", and as you can see it is staunchly Linnean – but it is decidedly non-ideological also, treating taxonomy as a means to an end and not as an end in itself. It is, in brief, yet another example of scientists simply refusing to take a stand for either "pure" view and eschew the "phylo-taxo revolution" in favor of, for the time being, reforming Linnean taxonomy: the entire case presented in this paper would be outright pointless in phylo-taxo (where probably Tubificidae and Naididae would have been scrapped by some author seizing on the opportunity to coin a name for the "tubificoid"+naidid clade - "Tubificimorpha" or whatnot, if the vanity fights about phylo-taxo definitions for certain Maniraptora in any indication).

As for a definition,

Kitching et al. (1998): Cladistics (2nd ed.). Oxford University Press, Oxford, UK. I have not read this but it probably will contain all you need.

Crucial is the distinction between "phylogenetic systematics" and phylogenetic taxonomy". The first is cladistics, the second is cladism. As I argued in detal above, your dispute is about cladism, that is, phylogenetic nomenclature, but only in a minor part about cladistics.

For if it were, how come the term "phenetics" does not appear in your discussion even once, or any other alternative to cladistic analyses?

And as I said, I prefer "phylogenetic taxonomy/phylogenetic nomenclature" to the ideologically charged "clad-ism". Regardless of what you call it however, there is a difference between systematics and taxonomy/nomenclature. Although it is hard to grasp for many judging from the times I had to rename "Taxonomy" sections in articles that were really and purely about the relationships of taxa and not about their scientific names. Dysmorodrepanis (talk) 11:20, 29 July 2008 (UTC)