Talk:Systematics

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Redirecting[edit]

I vote for redirecting to taxonomy if there are no other usages for the term. I kind of think there might be (non-biological), but I'm hard pressed to remember any of them. [user:Rgamble|Rgamble]]

I am working on an article on systematics as the study of multi-term systems as developed by John G Bennett. I did a page but then found that it did not exist![user:age blake]

Taxonomy not the same as Systematics![edit]

Wasn't taxonomy about classification and name-giving taxa, and systematics the study of organisms' evolutionary relationships? The latter is a research program and the former a practice.

Quoting [1]:

Systematics: the science of organizing the history of organismal evolution
     the science of ordering
  Identification: recognizing the place of an organisms in an existing classification
     Use of dichotomous keys to identify organisms
  Taxonomy (Nomenclature): assigning scientific names according to legal rules
     Recall discussion of ICZN Green Book (see also Phylocode homepage)
  Classification: determining the evolutionary relationships of organisms
        A "Natural Classification" will accurately reflect phylogeny
           Classification should be a hypothesis of evolutionary relationships

Shouldn't we divide taxonomy from systematics more clearly? Even in the taxoboxes? I noticed that the French wikipedia put a 'classical classification' (with Linnean categories) in their taxoboxes as well as a 'phylogenetic classification' (without Linnean categories). This seems like a good practice. Maybe we can do the same at other wikipedia's but call these Taxonomy and Systematics respectively. Fedor 09:39, 1 November 2005 (UTC)

Other Meanings[edit]

There is an article I am reading called, "Does Systematics Drive Old Testiment Exegesis? Or Can God Still Change His Mind? Questions of Method" by J. Daniel Hays. Not sure if this will help someone expand the article or put it somewhere else. I am still unsure what it means...66.68.215.101 15:15, 11 September 2006 (UTC)

ommision or editing of 6th paragraph[edit]

"Systematics is also of major importance in understanding conservation issues because it attempts to explain the Earth's biodiversity and could be used to assist in allocating limited means to preserve and protect endangered species, by looking at, for example, the genetic diversity among various taxa of plants or animals and deciding how much of that it is necessary to preserve."

Every word after "biodiversity" is unnecessary and is unrelated to the actual science of systematics. If that type of effort can be confirmed, then it deserves its own subsection.

I suggest an omission of this entire paragraph or at least a complete overhaul.

Science template[edit]

Systematics was added to this template. It is located under Life sciences. – Paine Ellsworth ( CLIMAX )  21:17, 11 May 2011 (UTC)

Systematics Is Not Classification[edit]

I see a serious problem with this treatment as well as the biological classification article, which links to this one. That is that the program of classification is very distinct from program of systematics, but the differences are not discussed (accurately) in either article. In brief, classification is based on the essentialist notion that biological entities represent "types" and that these can be sorted into classes based on their properties. They become members of the class and representatives of that type. This typological treatment need not be evolutionary, though in modern biology it often strives to be. In any case, the program of classification is waning in biology as we realize that classification is largely arbitrary and does not accurately reflect the dynamic and historical nature of life and evolution. Systematization is the endeavor to put biological entities into a system of relationships, which in the case of modern biology are evolutionary relationships. The objects are ordered as connected parts of a whole.

Unfortunately, these articles make pronouncements about classification being a part of systematics (e.g. the very old (and dated) Raven et al. quote) rather than a fundamentally different endeavor. These distinctions, while present in the older literature among theorists, did not come into the fore as an issue until the 1990s.

I think both of these articles should be updated. While WP is not the place to advocate one program over the other, it is true (and supportable with references) that classification and systematics are distinctly different and the former is falling out of favor while the latter is waxing.

This is also a sticky issue in regards to taxonomy, as some taxonomists prefer traditional classification-based taxonomies, while some (mostly systematists) prefer a rankless, phylogenetic nomenclature. It seems that most biologists recognize that taxonomic schemes should be largely evolutionary, but there is debate about whether paraphyletic groups should be allowed and whether taxonomic schemes need to exactly reflect evolutionary history, and if so, how the taxonomic schemes might work (e.g. phylocode).

I plan to edit these two articles and see if others agree.Michaplot (talk) 00:25, 5 July 2011 (UTC)

I agree in principle. It certainly is true that most people's views on the relationships between taxonomy and systematics amount to handwaving and views without perspective, and I would be very interested to see what you come up with and willing to assist if you can use any assistance. However, I have a reservation about what I understand to be your categorical views on the rejection of "essential" "types". (I am handwaving myself at this point, but be kind to me; I need it!) You say for example: "Systematization is the endeavor to put biological entities into a system of relationships..." But that presupposes a definition of the recognisable entities in question (and how does one recognise an entity except by phenotypic attributes arising from its "properties"?), and definition of relationships that one can recognise by their properties (whether formal or material) in turn? I am very interested in the concept of "entity" which seems to me to be fundamental to this discussion. For one thing, it seems to me impossible to think effectively except in terms of entities (including fuzzy entities, certainly) so we impose often arbitrary attributes on empirical fields of observation, just to be able to talk coherently as if there were such things as the entities we construct. One of my favourite examples, which has close affinities with biological entities, is the concept of a cloud, such as one you might see capping a mountain peak, or a ripple or eddy around a stone in a stream. Are such things entities? If they are, then what defines them, given that their components are constantly replaced? If not, then what prompts us to speak of them as such? Is the West Wind an entity? Compare such cases with organisms, species, and higher taxons? If they are entities, then how so? If not, then why not, and why do we speak of them as if they were? And if we did not speak of them as entities, then how could we speak of them? So, please feel not merely permitted, but actively welcome to rattle my cage at any time I could be of use. JonRichfield (talk) 07:27, 5 July 2011 (UTC)
Great point, JonRichfield. This is how I see it. (I am not sure how much background you have in systematics, so sorry if this is too simplistic.) So in traditional taxonomy, the wisdom was that only species are "real" (biological entities) and these could be identified (or verified) in principle by certain features that defined them (i.e. that they were interfertile and did not breed with other organisms). This so-called biological species concept has some problems, and other species concepts exist as well, but the point I am making is that I think early taxonomists (even and especially Linnaeus) recognized that a classification scheme was inherently arbitrary. Nature has no kingdoms, phyla, classes, orders, etc.
In systematics, we do have a bit of a tautology problem: a taxon (named group) may or may not be biologically real (by which I mean a lineage, a common ancestor and all of its descendants). But you have to have groups to study. Theoretically, you would have to "sample" every individual organism on earth and then by using phylogenetic methods, you could infer the relationships between them. Likely most organisms we identify as petunias would be more closely related to each other than most organisms we identify as whales, based on appearance.
In lieu of that, we often instead take a taxon and test whether it holds up as a biological group (is it monophyletic--an evolutionary lineage). Cladograms (tree diagrams of relationship) are seen as hypotheses of relationship to be tested and supported or refuted by additional evidence. This is how a tautology is avoided.
So in theory, we do not assume an entity (a taxon) actually exists as a biological entity and is not simply a made up entity. We attempt to test whether the entity is real or not. (This endeavor, of course, supposes that you accept patterns in nature as real and potentially discernible, that is, that you are a materialist, or a positive realist, and do not subscribe to a postmodernist or supernatural view of nature as completely non-existent or inscrutable.)
So, assuming that you accept that phenotypes or molecules or other data sources are present in organisms and that it is possible to gather these data in an unbiased way, then phylogenetic methods will allow you to determine operationally the pattern of evolutionary relationships among the organisms sampled. These then become the "entities" which in systematics are called lineages, clades or even lines of descent. The only other assumption you have to make is that the individuals you collected your data from are representative of group for which they are serving as a proxy. We normally have no reason to doubt, for example that the DNA sequence of a particular gene region in a fruit fly we ground up for our study is very different from the same gene region in every fruit fly of that species. But this is why science needs repeatability. Somebody should grind up some other fruit flies to test this assumption.
I hope this all makes some sense!Michaplot (talk) 08:48, 5 July 2011 (UTC)
It makes sense, but caution is needed to maintain NPOV, as you obviously know, since these are issues which although perhaps tending to a consensus are still hotly debated. The problem goes wider: the set of Wikipedia articles on classification, taxonomy and nomenclature is very muddled and needs some drastic sorting out.
Although some of its references may be old, the distinction at Scientific_nomenclature#Nomenclature.2C_classification_and_identification seems to me to remain correct, except that it does not make clear that nomenclature and classification need not be more than very superficially related, although they are in the Linnaean system. (In the current Phylocode proposals they are only tightly related in so far as binomials are to be kept.)
I'm not as convinced as you seem to be that there is some kind of contradiction between "systematics" and "classification". If classification presupposes some essentialist view, then obviously there is, but since Darwin, it doesn't. Currently biological classification is a way of (a) grouping things so that we can talk about them and name them (b) doing this in a way which reflects evolutionary history. I don't think that any reputable biologist seriously thinks that species are objective entities "out there" to be found, any more than higher ranks are. I think it's very wrong to write "We attempt to test whether the entity is real or not" as you did above; it's also not in line with the overall meaning of your text. What we attempt to do is to decide whether the entity is biologically useful in term of our current scientific theories, understanding and purposes. The last ("purposes") is crucial, particularly in relation to paraphyletic groups. I won't rehearse well-worn arguments, but merely point out that at the whole organism, natural history end of the biology spectrum, known paraphyletic groups remain useful for identification purposes, and are still being created, advocated and used. Of course it's important that this is done with as full a knowledge of the underlying tree as is allowed by current methods. Peter coxhead (talk) 10:00, 5 July 2011 (UTC)
Addendum: two nicely contrasting views can be found at Mishler, Brent D. (2009), "Three centuries of paradigm changes in biological classification: Is the end in sight?", Taxon 58: 61–67  and Stace, Clive A. (2010), "Classification by molecules: What’s in it for field botanists?", Watsonia 28: 103–122 . (As Stace's flora of the British Isles is the standard work, all UK botanists have to take his views seriously, whether or not they agree with them.) Peter coxhead (talk) 10:13, 5 July 2011 (UTC)
I will read the refs when I get a chance, thanks. My immediate impression is that I am puzzled that you would aver no reputable biologist would think species are real. This is a major issue, and I would say that most biologists I know (in fact I cannot think of any counter examples) accept species as real, but nothing higher, taxonomically. Granted, species are not conceived of in the typological guise that Mayr so detested, but rather as a population or set of populations with a shared gene pool. And granted, given evolution's ceaseless toil, one must be willing to accept that some species will be incipient or hybridizing itself into extinction, and there will be many cases where clear lines cannot be drawn. In short there will be lots of variation.
This I think is what some of the excitement in systematics is currently about. Not only are species biologically real, but now we have larger entities that are demonstrably real as well, insofar as existing patterns in nature can be identified, namely clades.
I would also take strong exception to your idea that classification has not been essentialist since Darwin. Classification is no different now than it ever was, save that we now, as you point out, try to base it on evolutionary history. (Darwin himself commented on the distinction between classification and what he called arrangement by genealogy, disparagingly on the former.) The salient feature of classification, however, is not simply grouping for convenience (that is far too weak a definition--there are many ways to group). Classification is grouping by characteristics that are conceived of as essential--as opposed to systematics, which involves grouping based on relationships of parts to a whole. Briefly the distinction is, classifiers see variation as a deviation from a theoretical prototype or "natural state" (Elliot Sober's term--he has written extensively on this issue). Their "job" is to see through the variation and sort individuals into classes. The flaw in this way of thinking is that each individual is seen as an instance of the class to which it is assigned, and the assumption is that we can learn something about the class by studying enough instances. This does work for some types of entities, like minerals or molecules, but does not work for species because species are, to quote Robert O'Hara (one of Mayr's students), "not independent replicates: they are parts of a connected tree of ancestry and descent, and they inherit most of the attributes in a way that stars and landforms, for example, do not."
Systematists see their "job" as documenting existing patterns in nature (history for the most part), and not creating classes in which to sort objects. Species do not have types to a systematist, and variation is not a deviation, it is the result of a dynamic process of change. The advent of evolutionary thinking after Darwin did not change the program of typological classification, it merely gave it new classes in which to sort. The conflation of systematics with classification may be a product of what O'Hara calls Group Thinking (that individuals are independent replicates of their group) which contrasts with Tree Thinking--the notion that evolution can be described (often with a cladogram) as a process with the focus on the evolutionary events that have occurred, not on taxa. You seem to advocate the Group Thinking mode of analysis.
One quick example: Group thinking (and the typological thinking that goes into classification) might have us ask, why does the genus Astragalus have so many more species than other genera of legumes? You might get a grant and spend your time studying the locoweeds to find what makes them so successful. Tree thinking (and systematics, in contrast to classification) would reject the notion that this necessarily means anything. The (dubious) assumption is that the genus Astragalus is somehow equivalent to other genera. To see if there was any biological meaning, you would need a phylogeny of the relevant groups and then you could see if in fact the lineage that we classify as the genus Astragalus really has more species than the sister lineage (in fact, it does not appear to). So saying Astragalus is a large genus (as WP does) is only relevant to human wrought arbitrary classifications, and has no biological meaning, though it seems to.
This issue is a can of worms. As much as I disagree with where I think you are coming from, my point of view is not relevant. I am at a loss about what to do on WP. I agree that the group of articles on these issues is muddled, and to make matters worse there is no firm consensus among biologists yet. Biology is in upheaval with systematics displacing classification, even at the level of nomenclature, which is sacred to some. I suppose this is just the latest phase of the trouble Darwin initiated. The big question is how to represent all of this on WP. It may not be possible at the present time, and we may just have to wait for scientists to come to more widespread agreement before WP can be updated. I am willing, however, as I indicated, to sometime in the nearish future, attempt at least to present a more up to date notion of the distinction between classification and systematics, without promoting one over the other.
One immediate problem I see on WP, however, which irks me is that most plant taxa (e.g. families) are described in terms of their taxonomy before or instead of their biological features. So, most articles begin "XXXaceae is [should be "are" but seldom is] a family of flowering plants with Y species and Z genera." I would prefer the taxonomy to be later in the article and the descriptions to focus on the biological entities rather than the definition of the name, as in "XXXaceae are an economically important group of herbs..."Michaplot (talk) 11:59, 5 July 2011 (UTC)
We could debate endlessly what "real" means here, I guess; I think it's a word best avoided in this context, although people don't. So our apparent disagreement may be just about what "real" means. [See also Mishler, Brent D, Species are not Uniquely Real Biological Entities, pp. 110–122, doi:10.1002/9781444314922.ch6 .] You wrote that species are conceived of "as a population or set of populations with a shared gene pool". But "shared" isn't a binary concept: given two populations, the degree of sharing can vary continuously from 0, so that the populations are good species with respect to one another, to the level at which sharing within each population is at the same level as between each population, so that they are clearly one species. Where you draw the line between these extremes is essentially arbitrary, which is why many conclude that species are, in this sense, not "real". (I can provide many references to this!). Ring-species are a good example, in that the end populations are good species w.r.t. each other but not w.r.t. the intermediates. And of course, as is well-known, your definition doesn't work for non-sexual organisms or populations which are geographically separated so that sharing gene pools isn't possible, and it doesn't work for extinct organisms, yet we need the concept of species in all these cases, to provide names, if nothing else. I can't find any serious writer about biological classification who doesn't know all of this and who takes an essentialist position. Who are all these "typologists"? "Classification is grouping by characteristics that are conceived of as essential": the only response I can make to this is "nonsense!". Mayr is a strong defender of traditional classification as against cladistic approaches yet he is utterly opposed to essentialism.
User:EncycloPetey persuaded me, rightly I think, that many Wikipedia plant articles spend too much space on classification and phylogeny and not enough on biological characteristics, so I agree with your final point, but, and it's a big but, the consequences of the genetic revolution in classification is that many plant taxa above species rank no longer have many biological characteristics in common to write about. Asparagaceae, for example, as circumscribed in the APG III system, are a very heterogeneous lot; Asparagales – an article I heavily revised – are even worse. What can you say about Xanthorrhoeaceae? (This bit Xanthorrhoeaceae#Biology and Ecology is actually wrong, and needs re-writing, because it's about the old Xanthorrhoeaceae, i.e. just the genus Xanthorrhoea.) The irony is that it's much easier to write descriptively about the old paraphyletic groups, because these were based on shared characters, albeit often pleisomorphies. (The old Liliaceae is a good example.)
So at present we can both agree that there's a big problem. Articles on topics like systematics, classification, taxonomy and nomenclature are often simply wrong (or at best muddled), and even if not wrong, are poorly referenced to modern work. The accounts of taxa are often over-burdened with classification and phylogeny, which are of little interest to the general reader.
What to do is another matter! Peter coxhead (talk) 17:14, 5 July 2011 (UTC)

Peter--completely agreed, the difficult question is what to do about this. I have been hesitant to edit some of these articles as I am keenly sensitive to my own biases, so it would be good to have a counterpoint in that endeavor. It is also hard to know where to begin.

As for the bigger issues, I think you have proven my point! I don't think "real" is a big problem to define in the narrow materialist sense. (I would say that a natural entity is real if it would exist in the absence of people.) In fact, the Mishler chapter you cited supports what I am arguing here. Mishler says in this chapter, "species properly defined are [emphasis Mishler's] real entities, but not uniquely real." What he is arguing is that species have no special status as a level and that species seem special because they are typically the most easily defined smallest inclusive group in a set of nested monophyletic groups (that is, below the level of species there is reticulation.) I remember discussing this with Mishler when I was a student, and he was keen on pointing out that an individual liverwort might fragment giving rise to a population of individuals all genetically derived from an original individual. This was a monophyletic group in his estimation. So his argument seems to be that species have no special status as there may be monophyletic groups smaller than species. So he sees the problem as a taxon problem--defining the smallest monophyletic group and naming it, if we think it is relevant to give it a name.

Mishler answers the question, "Are species real?" by claiming that, "all working biologists today think that the answer to [that] question is yes: species are real entities in some sense (although the grouping criterion considered to be the basis for their reality varies....)" And therein is the rub. Essentialist notions of species and other taxa are at the heart of classification. Systematics, on the other hand, despite being widely misconstrued, is about mapping, the pattern of evolution and does not inherently suggest a classification scheme. As Mishler suggests, we don't even have to give every lineage a name if it is not important to communicate about it.

As for who all these typologist are, they are legion. I can send you names if you want, but nearly every taxonomist who dabbles in classification is a typologist. My reading of Mayr, contrary to what you say, is not that he a defender of traditional classification and was opposed to cladistics (he coined the term). I think Mayr attempted to reconcile phenetics (another term he coined) with cladistics. He thought he should include both similarity of features and genealogy in a classification (he thought of himself as an evolutionary taxonomist, and such represented an initial attempt to reconcile tradition Linnaean taxonomy with evolution). He was a pioneer, but I think the thinking has evolved away from classification and phenetics altogether. His student Rober O'Hara argues convincingly that classification is not even viable for biological entities where it might be for non-biological entities.

As for a shared gene pool, Mayr was quick to point out that populations could be identified as part of the same species if they could potentially share genes. As I said, nature is messy and a ring species is a fascinating example of why essentialism does not serve biology. It is easy to tell that whale is a different species than a petunia, but different species of whale may not be easy to distinguish. A ring species may be impossible. These are incipient species as they have not achieved reproductive isolation. Still, these examples only prove the rule. I doubt if any botanist doubts that petals exist, but what about when petals grade into stamen or sepals. In those instances, it is hard to say what is a petal and what is not. This does not call into question the existence of petals as a genetic and morphological reality, it only shows we can't assume nature is working from a mold of an essential prototype of petal. The same can be said for any aspect of nature. Male and female sexes are undeniable, and yet in some cases the designation is obscure, even among humans. Don't confuse our difficulty in distinguishing what is going on with the idea that what is going on is not "real".

Finally, as for your "but", I would say that if a higher taxon is phylogenetically based, it must have at least one synapomorphy. If it is only DNA sequence characters, so be it. We can simply say that the particular group has been identified by molecular analyses. Some clades discovered by DNA are certainly counterintuitive in terms of the appearance of the members within them, but often subsequent analysis, with the benefit of hindsight, does reveal some theme or thread (inferior ovaries in Asparagales?).

I am enthusiastically in favor of focusing plant group articles on lineages with biological features rather than on taxonomic groups. The taxonomy can be included in the article but should not be primary. However, I have already had a user (Rkitko) question me about such changes. It may be a messy fight.Michaplot (talk) 22:13, 5 July 2011 (UTC)

Phew! We seem to have happened on a fertile field. I don't have time to respond immediately (mercifully, probably!) but one point to mull over: NPOV/OR. I appreciate the importance of those points in our context, but the policy on such things is still immature because the nature of the resource is developing even as the WP grows. WP is no paper, authoritarian document like 19th century encyclopaedias (and even those had far more NPOV/OR than our local obsessives would permit) We certainly cannot permit the article to degenerate into an edit war or similar counter-constructive abomination, but it seems to me that to produce an abridged or emasculated article as our idea of a definitive statement of the case, simply in the hope of avoiding arguments, would be unhelpful, even dishonest, as well as incompetent. If there is to be any cooperation on the product, formal or informal, I am sure that we can manage balanced statements in which as many aspirations as are relevant can be accommodated, without wasting effort and function on cat-fights. So far it looks good and constructive, I hope you will all agree. Cheers, back asap...JonRichfield (talk) 07:10, 6 July 2011 (UTC)
Oh, absolutely. The discussion between myself and Michaplot very much reflects the literature. What's important is that we all clarify our thoughts and gather sources so that we can present all sides clearly and fairly. Some of the existing articles are bad because, in my view, the editors didn't understand the issues. Others are bad because the editors didn't explain clearly. A few are bad because they are one-sided. Peter coxhead (talk) 07:39, 6 July 2011 (UTC)
Returning, for one last (?) time, to the issues Michaplot raised, a problem with discussing these things by text rather than in person is not quite knowing what the other person knows. So I'll assume that we both know the biology involved well. My problem is that you want it both ways. It seems that you want to say that species are "real" but also that "classification is not viable for biological entities". But as Mishler argues if you want to call species "real", then you have no reason not to call other monophyletic groups "real", and so you have a classification. It's not a rank-based classification in that it can't have a fixed number of levels, but it's still a hierarchical classification. In this very limited sense, compared to me, Mishler is an essentialist: he thinks there really is something 'out there', independent of human judgement, which is a species, and therefore there really are higher level clades. I think that there are organisms and populations which exchange genes to every possible different degree, varying in time and space; given that we need boundaries to talk about things, we have to rely on expert judgement to decide where to draw the boundaries in problematic cases.
The analogy is with the concept of a "heap". What exists 'out there' are almost infinitely variably different sized piles of things. We humans create the concept of "heaps" by imposing a fuzzy boundary. Some piles are clearly big enough to be "heaps"; some are clearly too small; some are uncertain. Precisely the same logical applies to "species", with degree of gene flow replacing size.
I shouldn't have used the word "arbitrary" in relation to deciding on the boundary, not because it's inaccurate, but because, like "real", it gets misinterpreted, and so is best avoided. Because some decisions as to boundaries are arbitrary (like whether a certain number of grains of sand constitutes a "heap", or what should be the legal age for drinking alcohol, or what should be the legal time limit for abortions) doesn't mean that they aren't important or can be avoided or don't need expertise.
Anyway, good luck with editing in this area! There are some more sources which may be relevant at User:Peter_coxhead/Citations#Classification.2C_etc.; I have been gathering them more as a preparation for some more edits to the monophyly/paraphyly/etc. articles than classification. Peter coxhead (talk) 07:39, 6 July 2011 (UTC)
Until the terms "systematics", "taxonomy", and "classification" are used with distinct and non-overlapping meanings in the litterature, it would be wrong of us to force a such a thing here on Wikipedia. Also, I'd like to point out that paraphyletic species are quite common,and as "real" as any other species. Claiming that strict clades are more "real" than paraphyletic groups united by clear biological features is in my view not bringing us closer to our aim of clear, concise articles. Petter Bøckman (talk) 16:36, 6 July 2011 (UTC)
I am not sure whether the sheer, calm rationality with which people have been discussing matters of great subtlety and on which they feel strongly, is more encouraging or unnerving! In either case I am deeply impressed. The contrast with the attitudes elsewhere... Oh well! Petter, I agree with you, but I don't think the intention (please do not let me attribute inappropriate intentions of course!) is to impose such a thing, but rather to propose suitable ways of looking at matters and using terminology. Commonly such attempts are futile, particularly in dealing with precise concepts and the precise applications of terminology, but every now and then a clear exposition does indeed set a foundation for the field, and the majority will adopt it. Such a result is so gratifying when it does happen that it is worth a try. Even if all we achieve is to document the nature of the differences clearly and cogently, that would be a proud achievement.
Oh, and as for the concern about whether all of us understand the necessary terminology, that is more of a concern for the articles produced, than for the discussion pages. People who cannot follow the discussion are unlikely to read on in an unfamiliar field, and if they do persevere and find themselves struggling, they can ask. No one will bite! After all, sometimes even competent participants will find themselves having to clarify their regional terminologies to each other. So what else is new? Cheers all, past my bedtime! Jon JonRichfield (talk) 20:48, 6 July 2011 (UTC)
Although Petter is clearly absolutely right about the literature, there are two different issues raised by a lack of clarity in sources:
  • What to write in the content of articles. Here it's perfectly clear: we try to reflect the literature in as understandable a way as possible.
  • How to name and organize articles. You just have to make one choice, just as librarians do in organizing books. Of course the content must explain alternatives, and there will be redirects, but the name of the article and way a related set of articles is organized just can't help making a choice. Thus by consensus at WT:PLANTS I recently changed the organization of articles within the Asparagales order; there are now articles about subfamilies such as Scilloideae when no such titles or articles on subfamilies existed previously.
What happens if different editors construct articles which should be part of a set based on different positions is that you get a mess, which helps no-one and doesn't explain any of these different positions properly. This is the situation, I believe, which currently applies to "systematics", "taxonomy", "classification" and "nomenclature" articles. So I'm strongly in favour of someone (perhaps User:Michaplot is volunteering!) coming up with a clear, sourced position – even if it's one I don't personally agree with, though naturally I hope it will be – and using this to organize the articles. Alternatives can then be discussed inside each of them. Peter coxhead (talk) 10:38, 7 July 2011 (UTC)
Going back to paraphyletic species, I cannot see how anyone can rationally disagree with Petter's view. If populations which exchange genes are "real", then any clearly defined grouping of such populations is as "real" as any other. The classic example is the brown bear: this is paraphyletic with respect to the polar bear, because it seems that polar bears evolved from within brown bears. But brown bear populations continue to exchanges genes with one another at a higher rate than they do with polar bears (although Arctic warming may be changing this), so the brown bear is as "real" a species as the polar bear, even though a cladogram will show the brown bear as a paraphyletic group of populations/subspecies. You can decide that you don't want to use paraphyletic taxa at any level, and there are good reasons to do this (but also good reasons not to), but you can't rationally say that you reject paraphyletic taxa because they aren't "real". Peter coxhead (talk) 10:51, 7 July 2011 (UTC)

Some thoughts, or if you prefer, lack of thoughts where thoughts are needed. What would one call a thing like that: a question? Well, never mind... Here some of the slots anyway, arising as I scan the recent exchanges:

  1. Let's stop talking about abstract, nearly metaphysical, concepts, such as taxons and species being "real", and instead speak of their being "meaningful" or "meaningless". The concept of reality is IMO too vague and arbitrary, even question-begging. Meaningfulness on the other hand is easier to assess err... meaningfully. For example, if neither the meaning nor its negation is true, one has a problem arguing about a statement being meaningful. And if it has no meaning, what good is it? It might help to think of "meaning" in terms of information states, whereas I don't know how to demonstrate the "reality" of a concept without first going into a challenging exercise of definition.
  2. On a related point, the cliché about only species being meaningful ("real"!) and higher taxa not, never has satisfied me, and by now it leaves me deeply suspicious. (As you can tell, I am no taxonomist/systematist, though interested in many aspects of the field.) For a start, looked at simplistically, on the same principle as rejecting the existence of an order, no such thing as a species exists either. Every definition of species, whether biological, behavioural, genetic or palaeontological, is arbitrary and open to objection. Right? In fact, we need to use different species and other taxonomic concepts for different problems, in the full knowledge that some of the concepts we use simultaneously, simply are mutually inconsistent.
  3. In spite of that, as I hinted to Michaplot, we have to go on speaking of such VDTs (my coinage for the nonce, meaning "Vaguely-Defined Things". I had thought of calling them FDTs for "Fuzzy", but many of them are vague beyond fuzziness. By VDT I mean something that we call a "Thing" (such as a species or a ripple, or even a notional category with not even its dimensions as yet defined) when we cannot cogently say what we mean, or even (yet) whether our concept is meaningful, but need to call "it" *something* because we don't otherwise know how to discuss our problems or ideas.) The simple fact is that we need a label to refer to, even if we do not yet know what we are referring to, or whether there is such a thing to refer to. We often find such difficulties in mathematical conjectures for example, where I might refer to the smallest number greater than 371, that is equal to the sum of the primes ranging from its smallest prime factor to its largest. I speak if this number as if it existed, but last I heard, no one had found one. Nor the smallest odd perfect number. Are such things "real"? Wellll... Are they meaningful OTOH? I think we might agree that they have certain kinds of meaning at least. Which is more than I could say for speaking of say, the largest prime, or the first member of the phylum Chordata. (Which for instance, if it had any meaning, would mean something different to a palaeontologist and a molecular biologist, I should say.)
  4. Granting that higher taxa have proved snares and delusions to generations of taxonomists and systematists, I don't see the concept of higher taxa as in any way less (or more) "real" than species; the question is rather whether we can refer to any of our definitions as meaningful: what does a given definition refer to? How would we decide whether there are empirical grounds for referring to it at all? Why is there a difficulty at all? And so on. IMO the problem is not that higher taxa are real or imaginary, but that although we can within reason refer to groupings at transitively and monotonically more inclusive levels, there is no consistent justification for asserting that a particular higher taxon that we assign is a consistent, well-defined structure. We find ourselves speaking of the Stangeriaceae with its embarrassment of lower taxa for a single species, in the same terms as Orchidaceae, with its lack of sufficient taxa. What we need is a usable notation for tree structures that will be proof against differences (and changes!) in branching depths and patterns.
  1. Speaking of Systematics as being in various respects different from Taxonomy I think is beyond denial. I am however far from convinced that the two are cleanly separable. Call them VDTs if you like. I am reluctant to get too deeply into this at present (luckily, I guess) but it seems to me that their subject matter is too intimately related for total separation. Feel welcome to prove me wrong in this matter. The distinction between them might work in a taxonomy of inventories and warehouse control, but in biology...? Tell me when to expect it! I am not an actual denialist, mind you, just canny.
  2. Mind you again, just because taxonomy is a sine qua non (I don't like the term "essential" in context) for systematics, it does not follow that one is part of the other. Then the alpha, beta... hierarchy is preferable. That sort of thing needs clear and up-to-date expression in a useful article.
  3. "classification and systematics are distinctly different and the former is falling out of favor while the latter is waxing."??? To me that makes no sense. Certainly classification always has been a specialist taste in biology, even though the products of such work always have been vitally important, because the sheer tedious slog work does not appeal to most biologists with their taste for "living" things. Certainly also, the fact that much classification has been based on early and unsound (not stupid, just established before cladistics and DNA sequencing tools etc were available) systematics means that much early work is to do all over, but it does not mean that either of the two is a sounder field than the other. "Falling out of favour" means what? That some prefer working in one to working in the other, or that one is less sound? I need either a bit of explanation or reassurance on some points there.
  4. "This is also a sticky issue in regards to taxonomy, as some taxonomists prefer traditional classification-based taxonomies, while some (mostly systematists) prefer a rankless, phylogenetic nomenclature." Yes. I mentioned some such points in the foregoing. But we have a range of problems here, of which the most immediate is how to deal with this in any WP article or complex of articles we might undertake. IOW: what are we to write? It must be comprehensible (including to anyone barely biologically and logically literate, who must at least be able to make sense of the intro para, before deciding that he would sooner carry a grenade in his briefs than proceed); it must be comprehensible and cogent all the way through for a competent biologist in a wide range of disciplines; it need not (theoretically must not) present any novelties, but must present the major points of view in a proper balance (NPOV etc). Am I sounding just a wee bit discouraging? Or just challenging?
  5. In the light of the previous point, I should recommend that we contemplate a larger set of smaller articles with heavy cross-linking. Future generations might unite our efforts, but trying to produce a single coherent version at this point seems a bit reckless to me. (But don't let me discourage anyone!)
  6. Note that though I have been in favour of the evolutionary point of view all my life as far back as I can remember, there is no theoretical reason why a taxonomic scheme should be wedded to Darwinian realities. It simply happens to be the easiest. Trying to imagine a non-Darwinian scheme of systematics now – that might be a bit more challenging, though I suppose it is theoretically possible, though I cannot imagine why one would want to do so. ;-)
  7. "...These then become the "entities" which in systematics are called lineages, clades or even lines of descent..." Well sure, up to a point, but that point is shifting and may seem very out of date in a few decades. Even in "higher" organisms we have many classes of examples of how "separate clades" can exchange genetic material or even merge entirely, (not even to mention the mind-bending complexities of endosymbiosis. (Hydrogenosomes anyone?) Those entities are not nearly as entitic as the essentialists would like them to be, are they?

I see that some of what I have said seems compatible with some of Peter C's remarks, not that I would claim to be representing his points in any form acceptable to him.

  1. The question of whether most biologists think species are "real" is far less important than whether they can defend their views rationally. As I said, forget "reality"; go for the meaning and meaningfulness. I bet that if you stopped a large arbitrary sample of biologists in the corridor and asked them for a defensible definition of "species", most of those that could rise to the challenge would be systematists, and even many of those would muff it badly. Any of them who denied the "reality" (see why "meaning" would be, not merely a better word, but a better concept?) of higher taxa would fall down on very similar grounds trying to assert the "reality" of species! And if they simply (and reasonably) denied no more than the "reality" of the Linnaean higher taxa and asserted the reality of clades, then they would find that very similar objections and meanings for clades would apply to species. I don't know about turtles all the way down, but this certainly is fuzzy all the way down!
  2. I see Michaplot had said: "Not only are species biologically real, but now we have larger entities that are demonstrably real as well, insofar as existing patterns in nature can be identified, namely clades." Which is consistent with what I have just typed, but let me once again insist on the advantages of "meaning" over "reality". Apart from anything else, "reality" is a hard thing to test in terms of useful assertions, whereas testing "meaning" guides one in formulating assertions.
  3. In context I am irresistibly reminded of one of Ogden Nash's essays into systematics:
Who's afraid of the big bad dream?
Things are never what they seem;
Daddy's bowler, Auntie's thimbles,
Actually are shocking symbols.
Still, I think, a pig's a pig -
Ah, there, symbol-minded Sig!

(Not that I agree, of course…;-) )

  1. Actually, I would take issue with Michaplot's view of the distinctions between classifiers and systematists. Not that I think his points are unreasonable, nor even perhaps the lines of thought of the sources he quotes, but that if one begins following up the meanings of the assertions to their bases, one finds that the differences begin to fade embarrassingly. Trying to discriminate between essences and relationships or even "existing patterns in nature" becomes more challenging than one at first might think. For example, statements such as "...variation is not a deviation, it is the result of a dynamic process of change..." come a fearful cropper over innocent questions such as "What is the difference between a 'dynamic process of change' and a deviation?" Given my personal (here irrelevant) background, I am inclined to see such things in terms of information states. And information states could as well reflect history as essence.
  2. That sort of thing might not be a show-stopper, but it certainly is the kind of challenge that any WP article on such subjects should be ready to meet reasonably, even if only by recognising and identifying its role in the discussion, even if it is relegated to a parallel article.
  3. "So saying Astragalus is a large genus (as WP does) is only relevant to human wrought arbitrary classifications, and has no biological meaning, though it seems to." Here I fall off the bus in a big way. That is a bare assertion and needs serious logical support. The question it responded to may have been badly formatted, even badly and illogically conceived, but it does not follow that the fact that the genus (read: clade?) includes many species, whereas other clades include various numbers of species, both greater or lesser, is meaningless, biologically and otherwise. There are whole ranges of possible forms of significance, and the fact that some lines of work proved sterile does not mean that the subject is sterile. (I might remark in passing that I come from fynbos country! ;-) )

OK, I had intended to work through the whole correspondence, but that won't work! Let's give it a rest for the moment. Cheers, Jon JonRichfield (talk) 17:01, 7 July 2011 (UTC)

I think much of the (apparent) dissent here is about semantics rather than any real disagreement on subject. I suggest Michaplot puts up a list of what he feels should go in each article, so that we may discuss it and see if we come up with a better situation that the current one. Oh, and one thing Gentlemen: Would you mind keeping this a tad less verbous? Petter Bøckman (talk) 17:14, 7 July 2011 (UTC)
Sorry Petter, speaking as a major offender ;-( However, it is a subject that depends on fine conceptual distinctions, which does not make for concise, definitive statements. Several of the issues are actually very substantial, and this is why it is so difficult to see how to structure the intended product. I for one will not be tackling the project as a primary author, though if anyone wants to bounce any ideas off me, either here, or offline, feel welcome. Cheers, Jon. JonRichfield (talk) 18:07, 7 July 2011 (UTC)
Lots to think about. I agree with Petter that paraspecies (or as Donoghue would call some cases, metaspecies) present a problem (e.g. the brown bear). Much ink has been spilled on this issue and I am not up on that literature. So the Mishler chapter that Peter C suggested solves this problem by pointing out that the species problem is really a taxon problem. Here would be how a strict PhyloCode toting cladist (and I am not one, mind you, but Mishler is) would solve the brown bear issue. The Polar+Brown bear clade receives one name: let's call it PoBro. The clade that includes only the Polar bears gets another name: let's call it Polar. All the other lineages get no name at all, unless there is a need to name those lineages. Paraphyletic groups are "real" as Petter says, in my opinion because the members did all descend from a common ancestor--but are treacherous biologically as they are often defined by plesiomorphies and may lead one astray.
I have been reading general discussions in textbooks and articles on the meaning and history of the terms classification, systematics, taxonomy, nomenclature, etc. My thinking is changing on this. It seems most authors see systematics as the larger category that includes classification. I do still feel (JonRichfield's comments taken into consideration) that classification is a qualitatively different endeavor than systematizing, but it appears that the ideas are not well differentiated in the literature. In fact, they are used variously by different authors.
I like Petter's suggestion. I will create a new section for this, but it may be a while before I can formulate a proposal for the relevant articles. Sometimes life pulls us away from WP.Michaplot (talk) 22:38, 7 July 2011 (UTC)
(Petter ≠ Peter; I wouldn't like Petter to be held responsible for my views!) I promise this is my last contribution to this thread. The problem with the cladist approach to the brown/polar bear situation is this. I see what an evolutionary taxonomist (to use Mayr's term) would call a "brown bear". I want to tell a strict cladist this. I have to say that I saw "a member of the PoBro clade which is not a member of the Polar clade". I think this is unlikely to catch on, particularly among naturalists rather than lab-based taxonomists. Peter coxhead (talk) 08:05, 8 July 2011 (UTC)

Proposed Revision of Systematics and Related Articles[edit]

As Peter C suggests, there are several issues to consider.

  1. What can we say about these topics? This may be a thorny thicket, especially as the literature has not done a good job of settling down to agreed upon meanings.
    1. This suggests to me we need to present these issues as an area of poor agreement in the literature, and probably provide a survey of the range of uses of these terms.
    2. If it turns out the various uses of these terms fall into distinct schools of thought, this will make things somewhat easier for us.
  2. How should we divide this material up into articles?
    1. I would be interested in someone starting a list of WP articles that we think fall into this category so we can have a central repository for what topics should be assessed and perhaps revised.
    2. Since these topics are a constellation nearly always discussed together in texts, it may be that we want one central article (and perhaps this one is the one as systematics seems, as far as I have discerned so far, to be the largest category). Other articles could be linked to it for more depth on the specifics.
  3. Systematics is fundamental to biology. As such it has been much discussed, and does generate heated emotions. (I once saw someone so overcome with passion they jumped up and berated a poor speaker at length in the middle of a 12 minute talk.) It would be good to have any prominent sources on these topics, both to build a reference list for the article(s) and so we are not leaving any stone unturned. So if you have any essential sources, put them up here.Michaplot (talk) 23:05, 7 July 2011 (UTC)
I'm personally more interested in the nomenclature/classification end of the spectrum, so I'm not sure that my list really belongs here. I'm wondering if we should start a new thread – NOT a discussion of the topic, but just the organization of the articles – at, say, WT:TOL.
As an illustration of the issues at this level, consider these (by no means an inclusive list):
I fixed some other redirects in this area by changing them, but this doesn't work for those above; the problem is deeper, namely the conceptualization of "taxonomy", "classification" and "nomenclature". I have re-worked Binomial nomenclature so that it is about exactly that and not related topics. Fixing "Linnaean taxonomy", "Linnaean classification" and "Linnaean nomenclature" is another matter; I'm not even sure how many articles there should be.
What I am clear about is that there is a hierarchy of inclusiveness: systematic biology > taxonomy > classification + nomenclature, but all four topics contain issues specific to themselves so that they are distinct, albeit related. Peter coxhead (talk) 08:21, 8 July 2011 (UTC)

Speaking as possibly the only non-taxonomist/non-systematist in the thread, please tolerate a heartfelt plea before getting too deep into actual writing. The plea is motivated by the fact that neither the facts nor the opinions lend themselves to the production of a monolithic document (yet!) The heartfeeling is motivated by having seen no end of projects where there never were the time or resources to do it right, but always was time and money to do it over (yet again falling foul of the same traps as before!)

The plea: For heavens' sakes let's do it top down! Let someone (or several in parallel) produce a skeleton article that if (hypothetically) expanded, would satisfy all parties and all readers, sophisticated in the subject matter or not. This article would be at most a couple of thousand words, or even a couple of hundred if some Medawar reincarnation were to materialise, who could name all the major subject themes in proper context, but without elaboration, maybe even without definition (details to be hammered out later. There might even be two types of expansions, simple, and professional... details details!)

Right! When everyone is happy with that skeleton (or root node or whatever you might call it or however you might construct it) not counting all the material he is bursting to add concerning any particular term, THEN only we carefully construct links from each technical term to a notional article that expands on that term. Each article would have links to any other article as required; the structure would be a far more general graph than a simple tree. Each article in turn would be another root article in its own right, and would stop as far as practical at every technical term that could be explained in another article without making nonsense of the flow of logic.

Then continue the process (sometimes in series, sometimes in parallel) until we have covered the field adequately, with only the gluttons for punishment still busy at the coal face. By that time:

  1. We should have an impressive product of teamwork (we seem to have promising material for the team.
  2. The product should be useful and easy to read whether by professionals or general biologists.
  3. The modularity and logic should make it easy to modify, and in particular to update the theme by modifying only an article or two at a time.

Comments? Jon JonRichfield (talk) 14:16, 8 July 2011 (UTC)

This is a major undertaking you are proposing. There are a whole range of articles that may fall under the "sphere of relevance" here. To name but a few (top rank): Biological classification, taxonomy, Linnaean taxonomy, evolutionary taxonomy, cladistics, phylogenetics, phylogenetic taxonomy, and (lower ranks) taxonomic rank, clade, monophyly, paraphyly, polyphyly, PhyloCode, evolutionary grade, wastebasket taxon and taxa in disguise. This list is by no means exhaustive. I'll try to help out, but being an "end user" taxonomist who quite confortably say brown bear and polar bear are two different species (heck,I use the term "class Reptilia" without hesitation), my imput may not be particularly welcome. Petter Bøckman (talk) 17:05, 8 July 2011 (UTC)

Yes Petter, you got that right for sure!!! Like you, I'll help where I can, but if everyone says: "No way, I can't spend three quarters of my working time on such a thing," I for one will not criticise. But it is a beautiful thought all the same. WP is full of near-parallel articles that ideally should have been parts of projects structured in such ways.JonRichfield (talk) 17:36, 8 July 2011 (UTC)

Two Minor Off-topic Questions[edit]

Sorry to ask this as it seems trivial. Still, these concerns are irksome.

In looking through many of the treatments on WP of taxonomic families and above, I have noticed that the grammar varies. In particular, I see some treatments that have singular verbs and others that have plural verbs, as in "Limnanthaceae are a family" vs. "Limnanthaceae is a family".

My understanding from the ICBN (and the ICZN too) is that suprageneric taxa are always plural, unless you are referring to the word itself. That at least is how the examples in the ICBN, article 18, seem to have it. APG, Stearn's Botanical Latin, the instructions to authors in the Botanical Journal of the Linnaean Society and Gledhill's The Names of Plants all agree. However, many published sources and WP do not. I suspect many of the published sources are written by molecular people or others with no expertise in taxonomy, or by authors whose first language is not English.

The other issue is, I see a lot of variance in the use of a definite article before the taxon name, as in "The Limnanthaceae are a family" vs. "Limnanthaceae are a family". As a grad student, my major professor, who was fluent in Latin, instructed me never to use an article before a taxon as Latin does not have articles (they are implied) and so it is redundant. Some taxonomists seem never to use an article (e.g. the APG), but others (e.g. Cronquist) seem to use it. I wonder if there is any guideline here or is it merely a matter of taste?

I have looked for sources on this, and have come up with not much. So my two questions for all of you are:

1) would "[XXXaceae] is a family" be proper? (I say no.)
2) "the XXXaceae" or simply "XXXaceae"? (I personally do not like the article, but my concern is whether this is simply a stylistic matter, or does the article change the sense of the name?)

I think that improper scientific usage makes WP look amateurish and unreliable, so I want to get other opinions about these trivial grammatical concerns before I edit these in my travels around WP. Thanks for any advice.Michaplot (talk) 05:10, 9 July 2011 (UTC)

Points well taken. No definitive answers, but it seems to me that a few observations and principles could meet the case closely enough for jazz.
  • Remember that it is not much good seeking guidelines on consistency in the existing articles; they are written by combinations of (sometimes mutually detesting) authors of varying competence and varying background. Some won't accept anything less than the official authority of the seventh edition of Lexicon Roma in the Codex marked 13 BC. In contrast their co-editors in the same article may insist that antecedents and concord is a communist plot that are on a parr with his spelling mafia. There are of course regional preferences, such as the English "Oxford outrow Cambridge", versus the American "The Red Sox is king again!" And on neither side of the Atlantic has there ever been much consistency.
  • Also, though the WP rule is that article titles should be singular nouns wherever practical, some articles still are wrongly titled, and many more have been so titled in the past.
  • As for the proper articles for taxa, I (personally, of course) recommend that:
  • When it is a clear case that a given usage is the correct one, you use it. Even if the anti-erudition Nazis descend on you in their wrath and get upheld, you did the right thing.
  • Anyway, academic correctness tends to unnerve the nit-pickers far more effectively than cheerful informality.
  • When in doubt, write as naturally and comfortably as you can.
  • Remember that whatever the Latin rules were, we are writing in (crumbling!) English, and in English, articles can be helpful (ask any Russian tourist!). Same with split infinitives and postfix prepositions as lampooned in Churchill's "arrant pedantry up with which we will not put!" Personally I rather avoid, not only splitting infinitives, but splitting other concatenations of words, such as verbs and their auxiliaries (eg "easily can manage" rather than "can easily manage") but I do that because it avoids certain kinds of ambiguity and confusion, not because it is correct.
  • Above all as Orwell said: Break any of these rules sooner than say anything barbarous.
In general, as long as you write as clearly and productively as you can, it will be OK, both within the WP community and for the purposes of punctilious readers. Try to be consistent and probably no one will even notice that you are writing carefully. It is not as though your writing and usages of technical or Latinate terms in this discussion so far have elicited howls of protest or derision!
JonRichfield (talk) 07:05, 9 July 2011 (UTC)
My points:
  1. We are writing in English, not Latin. The fact that words are of a particular number in Latin is a pointer to English usage but cannot be definitive. The fact that Latin has no articles is completely irrelevant.
  2. In English semantics often over-rides strict grammatical agreement. Many collective nouns are regularly used in both numbers depending on the sense intended (see Collective_noun#Metonymic_merging_of_grammatical_number). "Data" is a good example: the phrase "data is" gets about 178 million hits on Google; "data are" gets less than 45 million, notwithstanding the fact that "data" is the plural of the Latin word "datum".
  3. The use of articles in English is very complex and subtle; native speakers don't agree, and odd uses are a good way of picking out non-native writers. To me "the Asparagaceae are characterized by ..." is more natural than with the article omitted; I think because it's metonymic for "the members of the Asparagaceae are ...".
So I think that you cannot expect full consistency in this area – maybe in the German Wikipedia, but not in the English one! Peter coxhead (talk) 13:58, 9 July 2011 (UTC)

Source[edit]

Here's an article that could be used to cover some of the history:

Sorry, don't have time to add anything myself. – Maky « talk » 17:53, 6 June 2012 (UTC)

Template[edit]

Hello, I need a help from people with knowledge in systematics and taxonomy to discuss the Template:SysTax. This template was removed from the pages where it appears for discussion and improvment. Thanks Zorahia (talk) 15:22, 22 March 2013 (UTC)