Talk:Clade

Difficult article

I'm a casual reader of many of the science articles here on Wiki. This topic is very interesting, but the article is impenetrable to me. I thought to check the talk page for enlightenment, and find an absolutely gargantuan amount of nearly religious dissection of all of this. I can't believe that it can't be described well, even as a base abstract concept. A few illustrations would be VERY helpful, especially a side-by-side description of the same group, expressed as a clade, and taxanomically (which, I realize, may not be an actual word). If this is the current, or perhaps a current methodology, then there must be some intro textbook which makes this understandable. - superβεεcat  04:03, 28 June 2009 (UTC)

Most of what you so aptly describe as "nearly religious dissection" is commentary from one banned user, Mats Envall/Consist. Anyway, you're not the first to comment that this article is hard to follow, so I'll add an {{unclear}} template to the article to help alert other editors. Adrian J. Hunter^{(talk•contribs)} 05:32, 28 June 2009 (UTC)

Btw there's a Wikipedia tool called "clade" which draws these kind of clad-like diagrams. I was searching for it (I've used it before) and came across this article.--Tomwsulcer (talk) 19:50, 13 January 2010 (UTC)

The problem

The concepts of a clade, monophyletic, etc. are not the difficulty. I don't think they are hard to understand. The problem is the writing, which is confusing. Moreover the same editor worked on all these articles so they are all confusing. I don't want to pick on individuals. Let me say this. The goal is to impress not to clarify. I would therefore conclude the main author is on the junior side. That isn't his fault, is it? He wants to impress us but we want to be led by the hand. I can say what the article needs, too, a word-by-word careful editing with some rewriting. I can say why you aren't doing it also, because it is a lot of work. Well look, no pain no gain. Let's get the basic writing clear then we can worry about the nuances. I'm starting with cladistics. I plan to edit these several articles for basic writing and formatting. If you have a flare for writing I invite you to join me. We don't need more bad writing. You can always check what is said. I'm not rewriting the whole thing only making clear what is not clear. Then you can see to decide what goes in there. So, you will see small changes slowly happening here and there. I work slow. Ciao.Dave (talk) 05:34, 17 January 2010 (UTC)

In my view a substantial part of the problem is that there are several articles on key concepts in cladistics that all tries to cover the whole field. This article is about clades, yet it goes on and on about the cladistic method. The intro spends four sections on not explaing what a calde is. In order to make these articles coherent, I suggest sticking to what the title says:

• Clade is about the concept of monophyletic units. It should explain the tree-analogy and how clades are defined (stem-, node- and amomorphy-based), and mention crown groups briefly.
• Cladistics is about the method, and is where large chunks of this article belongs.
• Phylogenetic nomenclature is about naming, and is where the difference (and heated debate) with Linnaean nomenclature really belongs
• Monophyly, paraphyly and polyphyly all have their own articles, and there should be no need to repeat the whole concepts covered in these articles.

And for Pete's sake, don't use the idea that Linnaean taxonomy somehow "failed" to classify Archaeopteryx properly. It is simply not true, and the difference between between Gautiers and Owens definition of Aves is a case for the crown group article, not this one. Petter Bøckman (talk) 07:52, 21 January 2010 (UTC)

The parsimony, the parsimony

Cladistics is no doubt parsimonious and so is prose, especially encyclopedic. However, there is only so much you can do with parsimony. You can't apeak without speaking. You cannot explain the whole history of the world in a single introductory paragraph. When Hawking proposed to represent the unified grand field with a single variable, phi, members of the astonished audience exclaimed, phi? That's it, phi? So, I find the introduction to this article somewhat too parsimonious. I plan to expand it a little. Correct me if I'm wrong, but you (or I) need SOME space to explain things in a meaningful and connected manner.Dave (talk) 11:33, 20 January 2010 (UTC)

Updating updating taxonomy

This section is written from a moral point of view and the editor sprinkles it amply with prejudcial pronouncements. We are to see taxonomy as the dead hand of the past weighing on the minds of the living like an alp. The taxonomists because of their moral turpitude developed this rigid scheme to keep the young free thinkers of today in bondage but they like anyopne under 30 anywhere have developed their own savior study of cladistics with which they are going to save biology with the one and true way. One almost wants to throw the pope in there somewhere just for good measure. We have had to listen to this malarky for something over several hundred years through Martin Luther, Karl Marx the puritans and a host of other saviors now long forgotten. Excuse me, but I just can't resist. Cladistics is not a savior. It is not going to replace taxonomy. It is just a passing fad, and it is not in the slightest degree any less rigid than Linnaean taxonomy or any more progressive or anything else more. The reptiles include birds? Give me a break! We aren't going to see an end to paraphyly in my day or any of yours either. Cladistics contains a relatively objective assessment of the merits and shortcomings of each system, although one commentator remarks that it is not as objective as he would like. Compared to this it is the soul of blandness.

What we have here are two different systems with two different intents. Neither system by itself is adequate to scientifically portray life on Earth as we see it now. We want information that is presented by both systems and the classification of living things is making such adjustments to either as seems best for the data available at the time. We aren't interested in having the personification of cladistics contront the father figure of taxonomy in an adolescent or post-adolescent manner; many of us are beyond that now, me by quite a bit. I'm going through there and will try to add some equilibrium of language and viewpoint. If I fail back me up.Dave (talk) 16:47, 21 January 2010 (UTC)

I agree that the presentation could be much more neutral. Check the lead of Linnean taxonomy, which employs more measured language than what you see here. One problem is that it is far from clear that there is a well-defined school called Linnean taxonomy, with known precepts. There is a school of thought called cladistics, which (though this article doesn't make it clear) is not universally supported by biologists who work in the field of systematics. Though there *are* people who call themselves cladists, boiling down their exact teaching is not a simple matter. (Clades are common to the two schools of classification). I am not sure that there are people who call themselves 'Linnean taxonomists.' It might be better to use 'rank-based taxonomy', but then finding references to fill out the story might be quite time-consuming, since biologists who write on this topic (on whichever side) are not famous for their clarity or brevity. To avoid the difficult task of writing a full story complete with inline citations, it might be better to have a shorter and less-detailed article with big effort at neutrality. EdJohnston (talk) 17:31, 21 January 2010 (UTC)

I agree to bout of you. I think the key concept here is KISS - Keep It Simple, Stupid. Petter Bøckman (talk) 18:40, 21 January 2010 (UTC)

Edit: I have now rewritten and restructured the article entirely. I have substituted the examples with some that better illustrate the strong points of cladistics (Lobopodia), and one that clearly illustrate what happens when trees changes. I've put in a few sources too. I hope you like it. Petter Bøckman (talk) 09:56, 22 January 2010 (UTC)

I like it. It was a source of some chagrin to me that these earlier articles reamined in such a juvenile condition. I feel that I have to make them comprehensible before I can move on to other things that use the terminology. If I've done anything to stimulate your further interest that's just as good. My bottom line is clarity (and correcness of format). So, I will start in again at the top. If everything seems fine I will take off the clarity tag (which was on there previously). If not I will try to make it clear, but don't hesitate on my account to change any change I might make for the better. Since you are on the aricle, I may resort to inline clarity tags, purely to get you attention. Thanks for taking a hand.Dave (talk) 12:18, 22 January 2010 (UTC)

As you can see, English is not my first language. For this article to be good, someone need to check for obvious language bugs. Having grown up in the University system on academic publications, my English probably flows somewhat unevenly. Also, I'm not a cladistican, I'm actually a die-hard Linnaeanist, so some of the concepts may be a bit off. Petter Bøckman (talk) 12:47, 22 January 2010 (UTC)

Clade and ancestor

Well, I'm glad you addressed that confusing problem. Exactly what is an "organism?" I'm not sure I agree with you entirely. I've never seen any cladograms representing descents of individuals. My feeling is, since the term originated with concern for species, it should stay specific, as, in a sexual system, reproduction except for parthenogenesis and cloning never involves individuals, always pairs. But, as you have addressed these issues and it seems clear that some writers want to include individuals I cannot make up my mind. So, I'm not going to alter it further. If anyone wants to take a hand go ahead, as long as you produce an improvement. For the general public, you canot assume specialist knowledge or knowledge of specialist conventions and vocabulary, you have to give us cues that seem obvious to the trained biologist.Dave (talk) 13:03, 22 January 2010 (UTC)

I just followed what was already there (as i said, I'm a Linneaeanist). I think I've overheard some of the paleo-claditic people argue that since we only have individual fossils, not species, cladistics should always work from the specimen rather than from some hypothetical species. Perhaps that is the idea behind the ancestor-as-individual thing.Petter Bøckman (talk) 13:32, 22 January 2010 (UTC)

Well yes, but but of what is the specimen a specimen? An idividual or a species? Whether its an organism or a specimen of an organism, the same problem of semantics applies. I like what you have though.

The diagram is a problem

I've always read that Mammals came from Reptiles and there are numerous examples of fossil intermediaries betwee them. In our diagram they do not come from reptiles they come from amniotes. The caption implies that they come from reptiles. This is very confusing. Anyone got any suggestions? Unless we change the diagram or the write-up we are going to lose the reader on that one. PS I got to go now, I'll be on this for a day or two. There are some other problems.Dave (talk) 14:40, 22 January 2010 (UTC)

Cladisticans will have you believe that they have solved all problems by erecting Sauropsida, and that mammal-like reptiles weren't reptiles, so that that sauropsids cover all reptiles. This is only true as long as you stick to the crown group concept, which is not even universally accepted among cladisticans. I'll fix it right away. Petter Bøckman (talk) 14:59, 22 January 2010 (UTC)

No, wait, we should have a clade in the picture rather than o grade. I think the first one will do, but with text only on Sauropsida.Petter Bøckman (talk) 15:07, 22 January 2010 (UTC)

I'm back, sporadically. All right, I understand the diagram - I think. I will go on to the next thing, today sometime. When we get to the point where I understand it all, I'll be done. Small comment - I'm not sure the public would know the synapsids lead to the mammals. If you think of more improvements that would be nice. Later.Dave (talk) 19:55, 22 January 2010 (UTC)

I made a new picture to show the concept more clearly. I hope it solves the diagram problem. Petter Bøckman (talk) 23:47, 22 January 2010 (UTC)

Next item

I'm back. Other people might think this worrying about the fine points is a waste of time, but it isn't. The fine points make the difference between good work and just work. I'm willing to say we got past the diagram. But now, there is this obscure sentence:

"Contrary to the Linnaean systems where taxons are defined by describing key traits (apomorphies), cladisc taxons (clades) are named."

My understanding is that apomorphy is a cladistic term. But you said, "the Linnaean systems, where .... There are two different systems. A taxon is only defined by its apomorphy if that taxon is a clade within a clade. But, we're not talking clades, we're talking Linnaean. This is confusing, but it gets worse. You mean, taxons are not named? What is the taxon name? I suppose you mean that a taxon is defined by its key traits, but a clade is defined by its position in a line of descent. It leaves too much to be guessed, such as what you mean by definition, what you mean by naming. Also English does not have a word Cladisc. The equivalent would be cladish and that would be understood but it would be a neologism, people don't use it. Cladistic is better, but there are the other issues. Tomorrow.Dave (talk) 03:33, 23 January 2010 (UTC)

That sentence is wrong in so many ways ("cladisc" is a typo for "cladistic", btw).

1. "Linnaean" is an ambiguous term: it can refer to the way Linnaeus classified, the way his first-generation students classified, or to the current codes of nomenclature.
2. The "defining" (as contrasted with describing or diagnosing) of taxa is a separate issue. Cladistics does not define taxa, but neither do many other systems.
3. The part after the comma makes no sense.

According to many cladists, clades are real entities that exist in nature, independent of human perception. Apomorphies are a way of recognizing clades, but they do not define clades. The simple definition of a clade that I have always used is "a common ancestor and all of its descendents". Where things get sticky is "ancestor": do we mean an individual? a species? a clade? That's where the complexity comes in.--Curtis Clark (talk) 18:56, 23 January 2010 (UTC)

Yeah, I admit I bugged up that bit. The ting is we should have a few words on how cladistics "name" taxons rather than describe or define them, since the cladogram really define the clade and describes the units within it, and how taxons can be "described" without necessarily mention a single descriptive trait. We should also have a bit on how modern Linnaean taxonomists go about describing their taxons, and how the end result may or may not be a clade. How 19th Century biologists worked is really not relevant in this article. Feel free to write a better version than the mess I managed.

Tha "clades are real" stance hails back to Hennig if I remember correctly. It was a reaction to the prevailing taxonomic fade of the times, when species and genera were considered the only important stuff, and higher level taxonomy was largely ignored. Should this article have a historical section? Petter Bøckman (talk) 19:41, 23 January 2010 (UTC)

I would say, it should be somewhere, probably is. This article almost seems a little too narrow in scope for a general history - but that is only a first thought. We don't want to repeat things if we can help it. Maybe some WP look-ups are appropriate. If something is found, it can be linked in.Dave (talk) 00:49, 24 January 2010 (UTC)

Next item 2

Outstanding response. We are making progress here. Time for the next item:

"In node-based naming, taxon name A refers to the least inclusive clade containing X and Y."

This is a writing criticism. This is too parsimonious to make sense without a lot of thought and then not for general readers. What on earth is X and Y? You haven't said and unless we already knew we would never guess. The reader goes to us for definition and we start spouting letters at him. Well, PQR, and furthermore, YUV, and what is more JLZ. Ho ho. Second, can you detail what you mean by inclusive and exclusive? One always has to keep the audience in mind. I would say the sentence is aimed at the student in the field, but that is what the audience for the most part is NOT. Professionals don't need us, the public does, and they need us to explain it. We're doing good here so far. I was afraid I'd have to abandon it to the wolves and the vultures as carrion.Dave (talk) 00:44, 24 January 2010 (UTC)

Would "In node-based naming, a taxon name refers to the least inclusive clade containing the two species (or specimen) X and Y." make it more readable?

No. I found a clear write-up so I linked it as a main article and did a rewrite based on the main article.Dave (talk) 03:48, 25 January 2010 (UTC)

I agree on this article being too narrow for a history-section. I think that would be more relevant for the cladistics article. Petter Bøckman (talk) 09:02, 24 January 2010 (UTC)

There is something minimal there. It can serve as a starting point if necessary. How much do we want to say?Dave (talk) 03:48, 25 January 2010 (UTC)

What about keeping the two first sections of the "Taxonomy and systematics", and replace the rest of the text (which is really about cladistics, not clades) with some general examples of clades defines in different ways?

Hi, Petter Bøckman. Last year I should thank it would be useful to begin with a road map that lists what articles cover what, which of these to the heaving lifting for specific topic and which summaries and refer to the more details coverage, etc. At the time I thought the top-level would Taxonomy and/or Biological classification (both a mess); Cladistics and Linnean taxonomy at the next level. I also it would be start planning and searching for Cladistics first,as that: connects the top and below levels; potentially so long and complex that splitting into more detailed aspects be needed, and this would impact the structure of other parts of the package. I was and still am working on animal phyla, as I good 2 books from a local library and should use them as must as possible before another user reverved them. --Philcha (talk) 06:56, 25 January 2010 (UTC)

Hi Philcha! A top-down approach to this sounds reasonable. This really should be discussed somewhere else though. If Dave is up to it, we could consider starting a Category:WikiProject Systematics under the general Wikipedia:WikiProject Tree of life.Petter Bøckman (talk) 08:26, 25 January 2010 (UTC)

Hi, Petter, so far I've have found Wikiprojects not very useful - they seem to be bogged in processes, standards, etc. For a complex package of articles I've found 2-4 people with the will and the knowledge and/or ability to research it have been more productive. And we seem to have a good team of this enterprise: I've noticed your comments here are on the target; I used cladistics-based research on phylum articles and would like to improve my understanding of the core concepts, although I'd also have want to done a few more phyla; Martin is a paleontology PhD student and understands cladistics well, although he also has other objectives; and Dave's emphasis make it understandable to non-specialists is essential. --Philcha (talk) 11:11, 25 January 2010 (UTC)

I think perhaps the problem with the project-pages is that they outlive their usefulness, not that they are bad per se. I have no problems doing it here as long as we get to archive the top 9/10ths of this page first.Petter Bøckman (talk) 11:55, 25 January 2010 (UTC)

I've just remembered that there a "project-lite" known as a Task Force - to avoid bureaucracy but do useful work, e.g. working in what does in which articles, listing useful sources, etc. Cambrian explosion task force. I suspect a "Cladistics Task Force" or "Biological Classification Task Force" can be placed under Wikipedia:WikiProject Tree of life - provided the WikiProject doesn't get in the way. --Philcha (talk) 18:20, 26 January 2010 (UTC)

Defining clades

Dave, I noticed you made this comment in editing: English doesn't use "naming" to mean "definition" - I noticed your use of naming before - naming is purely assigning the name. This is very true, and confused the heck out of me in the beginning too. The thing is, in the technical jargon of cladistics, clades are named, not defined, or described. This should be mentioned in the article. Petter Bøckman (talk) 09:07, 25 January 2010 (UTC)

Good morning Petter. I see I'm not the only early riser, or maybe the times are different where you are. The young, they say, sleep so well because they have so fewer sins. Not true with everyone, I suppose. Anyway thank you for pointing that out. Are you sure now? If so it is the kind of subtlety that ought to be in here, so I suppose we might interpret that as an agreement. If you are sure. The panda paragraph needs some work. These "differences" that become obvious, have you got any in mind or is this another cladistic inscrutability? The cladists appear to be like classicists, they rejoice in the secret language of their field. That is why classics is on the decline. Not for everyone, but we thought it was. Similarly if cladistics is to be for the masses we have to make it so.Dave (talk) 09:28, 25 January 2010 (UTC)

Norway is GMT +1, it's nearing lunch here.

I don't have any sources on the "naming" (it may just be jargon), but when I was editing another article, I got a stern message from one of the cladist heavies saying "clades are named, not defined. I suppose it makes sense. The definition part is the tree topography, and a tree is a working hypothesis anyway. Thus, all that remains is to find the necessary anchors and supply a formal request to NumReg (the cladistic equivalent to Systema naturae). As consensus topography changes, the name may may be synonymized as a junior synonyme, but never declared a "nomen nudum" or "nomen dubium" as in Linnaean systematics.Petter Bøckman (talk) 10:21, 25 January 2010 (UTC)

I've been working on something else. I'm going to take a look now. Of course this should follow the conventions so naturally you should heed any stern messages from cladist heavies. But - we are trying to make articles comprehensible here. This is not a technical journal, would you not agree? So, we have to make compromises with sternness in favor of comprehensibilty, would you not agree? It ought to be possible to obtain prose that is not technologically too heavy and yet is not in error either. Technical writers do it all the time. This is NOT a biologist's or a cladist's vehicle for the publication of technical data. If it is any consolation I must say this sort of discussion is non-different from what goes on in industry in the technical writing occupation, including the name-calling, the spites, the stubborness, the blindness, the prejudice and everything else. People are just people, God bless them. Now, the main problem with these articles is lack of links and lack of references. Obviously the heavies or self-styled heavies don't feel they have to descend to that level, but according to WP policy they do. Since we started this discussion I have found a good many things explained in other articles without any hint of those articles in this or related ones. On this particular vocabulary item, the naming, I would say, let's put naming back where the lack of it has come to someone's attention but either put a note in or a link to an article explaining it. Just as in tech writing, these things can all be worked out. I was wrong about something else also: the character. The character is a technical term. But I was right about it not being comprehensible to the ordinary public. So, again, there should be a note in the article that uses it or a link on "character" to the article that does explain it. I don't know how much will you have to persist in this stuff but I would say go right ahead and I will back you up with he links and sources wherever I can. I will have to do this by successive passes. I will tell you what will happen if you, me and the heavies cannot work this out. First, not only will we not remove the tag at the top but others will go on there as well. And, they will stay on there until finally some editors that are sysadmins decide to take a hand. They will probably block new editors from the article. Then they will call for an expert. So, the heavies do not get to obstruct this article indefinitely. For myself I will persist as long as is reasonable. Then I will place the tags that seem reasonable - the sysadmins don't like it if you go overboard - and leave this as a special problem. But, we are certainly not at that point yet. Currently the article is really past the point of diminishing returns for me - I don't intend to spend all my WP time butting heads on one article when there is so much progress elsewhere I would like to see - but, I can do successive passes for a while. I always do manage to get SOME improvements in. But you know systematics is getting to have such an impact on all the biology articles that it is time someone took a hand. Step up to the bat, my friends.Dave (talk) 21:14, 26 January 2010 (UTC)

What goes in which article

OK, here's my suggestion:

• Discussion of cladistic vs. Linnaean systematics - Phylogenetic nomenclature
• The virtues and shortcomings of cladisics as a method - Cladistics
• The virtues and shortcomings of Linnaean classification - Linnaean classification
• Example of clades - Clades
• Example of grades - Evolutionary grade and Crown group (section on stem-taxons)
• Phylogenetic tree and cladogram - merge articles?

Petter Bøckman (talk) 14:35, 26 January 2010 (UTC)

Hi, Petter, I'm not sure whether the top-level articles is Phylogenetic nomenclature or Biological classification - one emphasises cladistics, the other emphasises Linnaean systematics, and these 2 articles mostly ignore each other. It might possibly to merge them, under Biological classification as that has the general title. If so, major sections would include the objectives of classifications (often different objectives), pre-Linnean classifications, Linnean classification, cladistics, and any other modern methods. Do you think something that this might work - or I am dreaming. --Philcha (talk) 16:21, 26 January 2010 (UTC)

Re Cladistics, I agree with "virtues and shortcomings of cladistics as a method", but would also give more emphasis to:

• cladistics as an "algorithm" for generating trees in other disciplines (anthropology, archeology, linguistics, textual criticism, etc.)
• some of the practical difficulties, such as unresolved polytomies or the difficulties of matching / aligning gene sequences.
• the fast development since about 2005 (? IIRC; I can find refs when needed) of large databases, more powerful computers and more sophisticated software.
• I suspect that explaining the most important items will force us to move some content into daughter-articles - for example I suspect Cladistics can explain monophyletic, paraphyletic and polyphyletic groups without all the "...morphies". --Philcha (talk) 18:05, 26 January 2010 (UTC)

The way I see it, Biological classification should be top level article It should detail biological description, the idea behind classification and have sections on Linnaeus and Darwin and a short historical overview covering various ways of classifying. The two immediate sub-articles should be Linnaean classification (which should cover modern Linnaean classification as well) and [[Phylogenetic nomenclature] + minor systems like phenetics and evolutionary taxonomy. 3rd level articles should be cladistics, clade, evolutionary grade, Crown group, Polyphyly and the Linnaean units (Phylum, Order etc). The relationship between cladistics and the Phylogenetic nomenclature is that the former is a mean to obtain the latter, so it makes sense to make cladistics 3rd level. What you say about other (non-biological) uses of cladistics should definitely go there, but we may find we need a page on PAUP. Does that make sense? Petter Bøckman (talk) 18:22, 26 January 2010 (UTC)

I'm delighted to see this discussion. However, someone has to act on it! I'm taking less of a content role now so that you savants can do your work but I will be serving as a backup for English and clarity and I can go on being an errand-boy for links and references. Don't be afraid to correct me if I err. Before I go much further with this I want to see what you actually do. Do something, however.Dave (talk) 21:20, 26 January 2010 (UTC)

Good to see you aboard, Dave! I think the first task should be to see if we want to split Linnaean classification into two articles, one on Linnaeus original system and one on the modern categorical systematics (with things like "tribus" and "Domain"). Doing that, it would be more easy to put much of the traditional stuff from Biological classification in the "Modern Linnaean classification" (oh, and we need a better name), and leave Biological classification-article a more general descriptive page that can easily be linked to other relevant articles. Does this sound sensible? Petter Bøckman (talk) 21:57, 26 January 2010 (UTC)

You seem to be taking the lead so lead away. On this subject I can edit but I can't innovate topics. I got here through linguistics. As to being on board I'm a sort of itinerant sailor boating from ship to ship that I can actually reach. If no one heavy opposes you, do what you like. If someone serious does - well, most everything can be negotiated.Dave (talk) 03:37, 27 January 2010 (UTC)

PS. I thought of a suggestion you might find useful - do a detailed outline for yourself. Then you should have a set of detailed outlines, which you can proceed to implement in the articles. I suppose the first step would be moving material around to the proper headings, then you would want to amalgamate or unify the text in each heading. Don't forget the illustrations.Dave (talk) 04:09, 27 January 2010 (UTC)

EDIT: I have now moved details of Linnaeus original system to Systema Naturae, leaving Linnaean taxonomy as a suitable reference for modern hierarchical systematics. It will need to be brushed up a bit, but the basis should be there. Petter Bøckman (talk) 14:59, 27 January 2010 (UTC)

Great, we seem to have agreed that we have a project and about its overall structure - including Phylogenetic nomenclature at the level of the structure, since there are non-cladistics approaches to phylogeny.

When preparing for big articles I build a Talk section for sources (e.g. Talk:Evolutionary_history_of_life#Sources_and_snippets) and another for an outline (e.g.Talk:Evolutionary_history_of_life#Outline_for_possible_rewrite - yes, the articles will be change as we find more, but we need some sort of plan initially). Since we're going for a package of articles this, I suggest a single page that collects this info the whole package. A Task (like WP:CEX) would be good provide we can set it quickly (Wikipedia:WikiProject_Geology#Open_tasks_and_guidelines looks quick and easy) and the relevant WP Project does not try to bog us down with standards, procedure, etc. Alternatively we could use the Talk page of one of the articles, although that risks from comments from people who are not to ready to contribute to the real work. --Philcha (talk) 21:41, 27 January 2010 (UTC)

I'd think main topics on structure belong in one central page, while the details belong under their respective sub-pages. I think the only correct place to have the top level discussion is under the talk page for Biological classification, but I'm open to alternatives. Petter Bøckman (talk) 13:36, 28 January 2010 (UTC)

Talk:Biological classification will be fine for the overall structure. If we need more than one attempt, we {{hide}} old versions. I think we should use a separate of Talk:Biological classification as our "library" of sources, divided into sub-sections and with brief notes (1 line) on the main points of each. --Philcha (talk) 15:23, 28 January 2010 (UTC)

I've started sections at Talk:Biological classification for structure and sources - all we need (?) now is start adding notes and surces. --Philcha (talk)

Pandas a bad example

"Differences between a Linnaean/apomorphy-based clades and a node-based ones become obvious when the phylogenetic hypothesis changes. When two species previously considered closely related are found to belong to different groups (e.g. the giant panda and the red panda), one of the species will be taken out of the Linnaean unit (in this case the "pandas" of the bear family) and transfered to a more appropriate unit or given it's own (the Ailuridae). In cladistics, the unit "pandas", the giant panda + the red panda remain, but the clade is now known to contain all bears as well as mustelids, racoons and kind, skunks and seals."

Well, I've been pondering this and researching it for a while. Ostensibly this is an example of how the classification changes if the phylogenetic hypothesis does; that is, some original classification was apomorpy-based but the classifiers saw the true light when they had a node-base cladogram. Then we have this very strange note, which denies there ever was such a classification, but this is only an illustrative example. What? Are we making up examples here? With all that expertise we have to invent examples, we can't find any real ones? I have before me from my collection a book by George B. Schaller (the original gorilla man) called The Last Panda. He has a whole appendix on the topic entitled The Panda as Panda. Detailing the history of the classification he points out that it was always troublesome. Some put the two pandas in either the bears or the raccoons and others split them between the two. So, there was no standard classification based on one synapomorphy. Some thought they were related, some not, based on intuition of apomorphies. The later node-based cladograms didn't offer us anything new or anything different, they only confirmed a more distant relationship. Therefore this is bad example; we want something that was apomorphic and is now nodish and is substantially different, if indeed we need such an example at all.Dave (talk) 03:27, 27 January 2010 (UTC)

Yeah, the pandas was a spur of the moment thing. The example that was used, old Aunty Archy was really very bad. Not only was it just used to ridicule Linnaean systematics based on a misconception, it also failed to show the real difference between the systems. What we really need here is a case of a group being moved to a different part of the tree in fairly recent time. The red panda was the only one that truck my mind. The point here is to illustrate the difference between the two basic approaches. EDIT: Previously unrelated groups found to be related (e.g. even-toed ungulates and cetaceans) does not really work as one is lumped into the other under bout systems. We need case where well known groups have been split up in recent time. The alternative is to explain the process without an example. Petter Bøckman (talk) 13:14, 27 January 2010 (UTC)

Where is the definition of 'clade'???

Where does it say "a clade is...[ + atribute (noun phrase)]"???

There's something wrong in this article. There's no real definition of clade. Instead, there's only a description of the procedures required to determine the existence of a clade, the abstract nature of the clade, etc. But what is really a clade??? Not even a person who is somewhat familiarized with taxonomy would be able to tell what they're talking about in the article if we only consider writing (composition).--Quinceps (talk) 04:04, 29 January 2010 (UTC)

The definition is in the header: a single "branch" on the "Tree of life", a group composed of a single ancestor and all its descendants. Would it be better if it was restated in the first part of the "definition" section? Petter Bøckman (talk) 05:39, 29 January 2010 (UTC)

Fixed the definition. Here are diagrams that may help improve the article.--Espoo (talk) 12:41, 3 May 2010 (UTC)

But is this definition actually correct, i.e. reflective of current usage? It implies that a clade must include all the ancestors. But many (if not most) uses of clade-based descriptions (e.g. phylogenetic trees) deal only with extant species forming the terminal nodes of the tree. I think it's actually very difficult to write down a definition which covers the range of current usage. I think the definition should be something like "A clade is a group of taxa which includes all the descendants at the relevant level of their closest (most recent) common ancestor", where "relevant level" varies: it might be a requirement for all the taxa to be extant, or it might be a requirement for all ancestral taxa to be included. I don't think that clade is always used in a way which includes the ancestor in the clade, as the definition implies. For instance, the cladogram of crocodiles given in the article does not form a clade according to the definition if the clade consists of the 8 genera listed there, since no ancestral genera are included. Peter coxhead (talk) 18:26, 6 December 2010 (UTC)

By the very definition of a clade, it does include all ancestors at least down to the last common ancestor (node based), and sometimes further (stem based). This means that all clades above species level will include either extinct species or grade species. In modern biology usually existing species are relevant and mentioned, but the extinct members are implied implicitly. Most extinct species will remain unknown anyway. This is the case in the crocodile cladogram, where the hypothetical species X representing a node or brancing off from any point in the tree is omitted for the sake of clarity. Imagine the job of making a cladogram of the full vertebrata, with all known extinct groups!

In palaeontology a clade is usually given with a mix of living and extinct species or with only extinct ones. There is no requirement for any of the taxa in a clade to be extant.Petter Bøckman (talk) 22:20, 6 December 2010 (UTC)

When you say "by the very definition of a clade", you mean, I believe, a specific referenced definition which you are arguing is THE correct definition, rather than a definition which attempts to set out the way in which the term is actually used in the literature. Of course I agree that there are definitions of clade (e.g. in the PhyloCode) which includes all ancestors (with or without the nearest common ancestor). But this definition means that, e.g., I should not write "The eight extant genera of crocodiles form a clade." The literature is full of sentences of the form "the <insert number> <insert taxa description> form a clade" where the specified taxa certainly do not include all the known or unknown extinct groups. Now you can say that these authors are using the term "clade" incorrectly (or perhaps the verb "form" incorrectly), but you can't say that this isn't how the term is used – do a Google search for the exact phrase "genera form a clade" for example. This argument applies with even more force to "monophyletic group" which is (I think) held by the majority to be synonymous with "clade". NPOV surely requires that we try to explain how a term is actually used, rather than how we think it should be used. On the other hand, it's very difficult to do this, because the literature is actually quite confused: terms have changed their usage from the original Hennig ones; palaeontologists use terms differently from those concerned only with classifying species for which genetic data is available; some authors have axes to grind (e.g. Mats Envall wants us to use "holophyly" instead of "monophyly"); and so on. I don't have a magic solution! Peter coxhead (talk) 22:56, 6 December 2010 (UTC)

I think the word "form" (as you pointed out) is the culprit here, rather than "clade". In mathematical expressions, the sentence "X+Y+Z form group A" means that A contains just the tree. In phylogenetic taxonomy (of which I am no great fan) "form" is used synonymous to "mark", "demarcate" of "define". The convention is to name two "nodes" to delineate the clade, e.g. Crown-mammalia being Ornithorhynchus + Homo. I think you are right in that this little language peculiarity should be explained. Care to write a sentence or two? Petter Bøckman (talk) 13:11, 7 December 2010 (UTC)

I agree with Mats Envall, though I think he may have put his point more diplomatically. As I understand it, a group of organisms is polyphyletic if it does not have a single common ancestor that is a member of the same group. A monophyletic group is not polyphyletic (so its members are all descended from one common ancestor that is also a member of the same group). A holophyletic group is monophyletic and contains all the descendants of the common ancestor. A paraphyletic group is monophyletic but does not contain all the descendents of the common ancestor. I first saw these definitions, or their close equivalents, in a book written over 20 years ago that I can't now find. Even older texts (going back to the 19th century) classify taxa as either polyphyletic or monophyletic, so I'm sure these are the classical definitions. To conflate the terms "monophyly" and "holophyly", as Wikipedia currently does, is thus historically inaccurate and potentially confusing as well as being unnecessary. The term clade being synonymous with holophyly means we have two terms for the same concept. Either will do. The question of whether we should employ the current or the classical usage may be avoided were we to provide both the classical and the modern versions of the word in the definition of a monophyletic group, then avoid using the term elsewhere and use the terms "clade" and "paraphyletic group" as and where appropriate. Dendropithecus (talk) 03:18, 2 October 2011 (UTC) Dendropithecus (talk) 03:53, 2 October 2011 (UTC)

The usage of the term "monophyletic" has clearly changed; that is not disputed. "Monophyletic-pre-Hennig" = "monophyletic-post-Hennig" + "paraphyletic". There was an attempt to keep using "monophyletic" in the old pre-Hennig sense and substitute "holophyletic" for the new post-Hennig sense, but this has not caught on. Wikipedia policy is clear that we must reflect actual sourced usage. So we don't have the choice you imply above. However, I agree that in all appropriate places (e.g. this article and the ones on the three "-phylies") there should be mention of the change in historical use.

There is another, quite different problem, which is that the terms "monophyletic" (modern use) and "paraphyletic" are actually quite difficult to define accurately, particularly "paraphyletic". The literature is confused (not to say confusing). This creates a problem on Wikipedia, since we cannot chose one usage where the literature has several inconsistent ones (this would violate WP:NPOV), nor can we produce our own original clarifications of the different usages (this would violate WP:NOR) – we can only report sourced, consensus clarifications made by others. I can only say that I haven't found any such yet.

(I'm not saying that there aren't good, precise definitions – I find Podani's excellent [Podani, J. (2010), "Taxonomy in Evolutionary Perspective : An essay on the relationships between taxonomy and evolutionary theory", Synbiologia Hungarica, 6: 1–42], and his distinction between e.g. "monophyly" and "monoclady" is useful, since others use "monophyly" sometimes to mean his "monophyly" and sometimes his "monoclady". But it's clear that most biologists haven't adopted Podani's terminology, so we can't here.) Peter coxhead (talk) 12:41, 3 October 2011 (UTC)

One thing is clear from what you say (thank you for that, by the way). This is that there is no term we can use to express the classical meaning of monophyletic. This is a ridiculous situation and one that could and should have been avoided. but, as you say, there's nothing we can do about it now within the rules of Wikipedia. You say (and I don't dispute this) that Wikipedia's rules mean that we can't now use the pre-Hennig meaning of monophyletic, but does this mean we have to use the post-Hennig meaning? Since (correct me if I'm wrong) "monophyletic-post-Hennig" = "holophyletic" = "cladistic", it seems to me we could use one or both of the last two while ignoring the term "monophletic", except in its definition. For example, the sentence that starts "A clade is termed monophyletic, meaning it ... " would read "A clade is termed holophyletic, meaning it ... " or just "A clade ... " Is there anything in the rules to prevent us from doing this?

I wasn't aware of the confusion around the definitions of "monophyletic" and "paraphyletic". (Do you have any references I could follow up to give me a better idea of the problem?) If we can't find a single, referable, definition for either, couldn't we stretch the rules slightly and create one that conveys the consensus of the current usage, so that it's consistent with the references we have, then wait to see if anyone objects? What other option is there? Dendropithecus (talk) 08:33, 4 October 2011 (UTC) Dendropithecus (talk) 08:55, 4 October 2011 (UTC)

I've started to collect my thoughts and references on some issues with current articles in this area at User:Peter_coxhead/Work/Phyletic_terminology. It's far from complete or sorted out at present, but may be useful. Peter coxhead (talk) 09:00, 4 October 2011 (UTC)

Confusing article (and some examples?)

The article was tagged with a "confusing" tag in 2009, well before the current rewrite. It is still confusing? How do we go about determining if it is now an acceptable read? Ask my old Mom to read it? Just remove the tag?

I just removed an example of a clade (Archosauria i think it was meant to be) from the intro. I did not remove it because it was a bad example, but because it was not worded to in reference to phylogeny and because I feel the intro is not the place for examples. Examples are a good idea though. Should we dump some of the text on history (which is really more about cladistics, not clades per se) and put in some examples in stead?--Petter Bøckman (talk) 17:32, 5 May 2010 (UTC)

Seeing that there has been no new edits for a while, I now remove the "comfusing"-tag.--Petter Bøckman (talk) 10:39, 23 August 2010 (UTC)

Cambrian Explosion

The C.E. article would be enhanced by addition of the relevant parts of this article. Alas, I'm not knowledgeable enough to do so. Imagine Reason (talk) 10:32, 22 July 2011 (UTC)

It's easy. The way I do it (or did it, once) is as follows: Open a blue edit box for the relevant section of the source article; in this box, highlight the parts you want to copy and copy them; cancel the edit; open an edit box for the relevant section of the target article and paste your selected text where you want it, then, to finish, type a brief description of what you've done in the "Edit Summary", ending with four tildes, select "Show preview" and, if it looks OK, "Save page". Dendropithecus (talk) 04:48, 2 October 2011 (UTC)

The edit summary needs to state the source of the copied text for compliance with Wikipedia's author attribution requirements, per Wikipedia:Copying within Wikipedia. Adrian J. Hunter^{(talk•contribs)} 05:08, 2 October 2011 (UTC)

Diagram description problem?

"The green box is not a clade, but rather represents an evolutionary grade, an incomplete group, because the blue clade descends from it, but is excluded."

Isn't the blue clade ascended from it rather than descended? ScienceApe (talk) 12:42, 4 September 2011 (UTC)

I understand what you're saying – there's ambiguity between "descent" as in Common descent and "descent" as in progress downward. But it seems to be common to draw evolutionary trees this way, with the oldest taxa at the bottom, like the trunk of a botanical tree. I've piped a wikilink from "descent" to Common descent which I hope will avoid confusion, but there might be a better solution. Adrian J. Hunter^{(talk•contribs)} 15:14, 4 September 2011 (UTC)

I wrote that. English is not my first language, so if it is bugged up, I'm to blame. Feel free to edit it to a correct expression. The intended meaning is along the "hails from" or "have evolved from" lines. Petter Bøckman (talk) 18:53, 4 September 2011 (UTC)

Here's a useful, but rather subtle piece of English usage. "A descends from B" can have two meanings: geometrical, i.e. A goes downwards from B; and kinship, i.e. A is a descendant of B. However, "A is descended from B" always has only the second meaning. So when kinship is meant, it's better to use "is descended from" rather than "descends from". I've edited the article accordingly. Peter coxhead (talk) 08:42, 6 September 2011 (UTC)

Thank you, and thanks for the English lesson! Petter Bøckman (talk) 09:36, 6 September 2011 (UTC)

Ah, yes, good idea. Adrian J. Hunter^{(talk•contribs)} 05:10, 2 October 2011 (UTC)

Conceptual definition problem?

The problem with the concept "clade" is not just a matter of what "the green box" represents, but what the concept itself represents. The problem is that the concept denotes a contradiction, that is, a paradox (called Russell's paradox). The problem is thus that the concept does not have a consistent definition. It does thus not have any unambiguous kind of objects to attach to. The problem with the concept is thus that it is contradictory. It can't be defined without contradiction, and things of this kind can't be found without contradiction. The concept does thus denote a non-existing object, like the concept "God". Defining this concept is thus just as impossible as defining the concept "God". Cladists can thus just put their hope in Sjöö. He may be the realist that can break this "natural" barrier between consistency and self-contradiction. If Sjöö can do anything else than deleting sensible comments, then he may be the leader of cladists into the future. Until then, he is just a defender of a sect, that is, cladistics. Sjöö and other cladists have tried to define this concept (i.e., clade) for about 15 years by now, when will they be discarded as the paranoics of the sect "cladistics" as that they are? 80.216.133.188 (talk) 00:46, 25 December 2011 (UTC) Mats Envall

(BTW, Adrian Hunter appears to be nearly as simpleminded as Sjöö is.) 80.216.133.188 (talk) 00:50, 25 December 2011 (UTC) Mats Envall