Tuesday, December 29, 2015

Aubert's analysis of phylogenetic terminology, part 2: definitions

Continuing the discussion of this paper from here. Originally I had the idea of going through the pages in sequence, but it may be more productive to tackle one by one what appear to be the main claims of the paper as I see them:
  • The various definitions provided in the paper are in some way better than the ones that are currently accepted.
  • There is no relevant difference between the systematics-relevant relationships and structures existing at any level of the diversity of life. (E.g. mother > daughter is completely equivalent to bony fish > land animals - they can all be drawn as diamonds and arrows, right?)
  • A strictly phylogenetic classification is formally impossible.
  • Cladism is part of structuralism and therefore characterised by "anti-realism and a metaphysical way of thinking".
  • Cladism is built on biologically unrealistic assumptions that have been empirically falsified.
  • There exists an objective approach to delimiting paraphyletic groups.
  • It would be preferable to have two parallel classifications, one of clades and one that includes taxa that are allowed to be non-monophyletic.
So this might turn into seven separate posts, although the last few will perhaps be short. This is the first one, dealing with the definitions, and it got rather long.

The definitions themselves

About the first two thirds or so of the present paper consist of a mixture of "lemmas", "definitions" and "observations" interspersed with helpful figures. As mentioned before, the latter consist of diamonds connected by arrows and serve to illustrate the definitions. To get a flavour of the text, consider this example:

This is accompanied by a figure showing diamonds connected by arrows and a group of diamonds marked to illustrate the concept of "lineage". Here is an alternative way of providing the same information:
A lineage is a line of descendants without gaps.
This alternative is (a) shorter, (b) easier to understand, and (c) fully equivalent in the sense of not missing a iota of information or precision compared to the original. The question is then why one would choose to express what boils down to perhaps two to three pages of really simple, one-sentence-ideas with thirty pages of lemmas, indexed place holders, set theory and suchlike.

Perhaps this is a bona fide attempt to be 'precise', but a reader who suspected that it represents an attempt to intimidate and bamboozle the reader with math, to make them think that something much more profound is going on than there is, could at least not easily be called unreasonable. Curiously, Aubert himself asks in a later part of his paper "whether the criticisms against [sic] classical evolutionary systematics do not come from an illusion of precision due to the use of mathematical tools in cladistic analysis". (Pot, kettle, black?)

Anyway, some of the definitions are trivial or irrelevant and clearly only included for the sake of completeness, while others are directly relevant to the controversy around whether partial clades should be formally accepted as taxa. Concentrating on the latter:

Lineage = As mentioned above, a line of descent without gaps. Aubert illustrates it in a way that strongly implies a linear, unbranched shape, with only one item per generation. I find this odd because to me such a lineage would be incomplete, but I guess that just means that I am a cladist. What is even more unusual, however, is that Aubert also defines the term in a way that it is satisfied with a single individual. Surely that does not fit the way this word is generally understood.

Ancestor =  An item is an ancestor of another item if they are connected by a lineage. This is soon followed by an interesting "observation": An ancestor is apparently also its own ancestor, at least if I interpret the wording correctly. This is called at the same time "counter-intuitive" (true), "trivial" (not to me, perhaps because I do not believe that a single item is a lineage), and "greatly facilitat[ing] the formulation of many properties thereafter". It is nice that Aubert will find this to make his definitional jiu jitsu easier, but that does not necessarily mean that it makes biological sense. I mean, if I define rock as cheese I will also find it easy to prove that the moon is made of cheese, but most people would quite sensibly take issue with my definition.

Group = In Aubert's usage, any random assemblage of items in his graphs that he draws a line around. A cladist would, of course, consider anything non-monophyletic to not really be a group in any useful or meaningful sense. Often in this context people are asked to consider similarly nonsensical non-groups outside of the tree of life but likewise defined only by lacking a trait such as non-Hindus or shirts that are not white.

'Monophyletic' group = A group that contains its own common ancestor. Clearly here the currently accepted definition in the vast majority of scientific journals, conference talks, textbooks and university courses is a different one. I will subsequently scare quote this definition, so if the quote marks are not there I mean the widely accepted Hennigian definition.

At this point Aubert worries about this definition allowing groups that contain items and their common ancestor but not the intermediate ancestors, so he consequently clarifies:

Continuous 'monophyletic' group = A group that contains its own common ancestor, and all of whose members are are connected to the common ancestor by descent through other members

Ancestral group = A 'monophyletic' group containing a common ancestor of another group. We are now really, really, really deep in begging the question territory as far as the controversy between cladists and their opponents is concerned. Not only is such a group not really a group in any meaningful sense, most of it isn't ancestral to the subclade Aubert would exclude from the 'group' in the first place.

Directly ancestral group = The same but the ancestor-descendant relationship between the ancestral item in the so-called 'ancestral group' and the common ancestor of the other group is direct, without intermediaries.

Exclusively ancestral group = The descendant group has only this one ancestral group, i.e. it is not derived from a cross between two different ancestral groups. Here Aubert seems particularly concerned with endosymbiosis. I will never understand why so many people believe that this is relevant. The chloroplasts are a monophyletic group that has colonised eukaryotes, and the plants are a monophyletic group of eukaryotes that has been colonised by a clade of cyanobacteria. This appears to be another case of conflation, in this case of systematics-relevant lines of descent with systematics-irrelevant horizontal gene flow. One could just as well claim that a human needs a new family name after getting a heart transplant. Curiously, once more there is a place in the paper where Aubert warns against precisely that kind of conflation himself.

A mere four pages after 'monophyletic' we come to paraphyletic, polyphyletic, and holophyletic, the former two defined the usual way, the last the suggested alternative to what nearly everybody today calls monophyletic. Aubert now provides two 'utilitarian' arguments for changing monophyletic to holophyletic.

First, if the paraphylists cannot use the word monophyletic to mean either monophyletic or paraphyletic, they "[have] no other term to account for their concept" and "cannot assert their point of view". From a cladist perspective, that is a feature, not a bug, because they consider the concept unhelpful and the point of view wrong. Again: like non-Catholics, not really a group, etc. One wonders also, given how frequently paraphylists make up new terms, why they could not just have made one up for this eventuality.

Second, the either monophyletic or paraphyletic meaning would be "useful in studies of unrooted phylogenetic trees where precisely [sic] it is de facto impossible to distinguish holophyly and paraphyly". Maybe there are dozens of people out there who have that issue, but I am not aware of a single situation like that. Towards the end of the relevant section Aubert mentions that somebody has already made up a new word for that situation (clan), thus undermining his own utilitarian argument.

Heterophyletic = What the rest of the world calls non-monophyletic.

Canonical holophyletic group = Associated with a paraphyletic group, what it would turn into if all its missing sublineages were added.

Complementary group = If I understand correctly, the subclades left out of a clade to circumscribe a paraphyletic group.

Degree of paraphyly = Number of subclades that had to be left out of a clade to circumscribe a paraphyletic group. A similar degree of polyphyly is introduced later.

On page 19 Aubert defines holoclady and heteroclady to solve the same imaginary problem in exactly the same way as Podani and Vanderlaan et al. before him. From a cladist paradigm, the question whether a valid group includes only extant terminals or goes right down to the ancestor is a complete non-issue; it is only if one desperately wants to accept paraphyletic taxa that it even arises. What is more, we now have three sets of terms for the same thing. Decrease the confusion? Improve communication? I wish.

It is interesting to note that Aubert comes perilously to a cladist view when discussing monophyletic, paraphyletic and polyphyletic groups of terminals:
This means that a holocladic pattern suggests the existence of a real situation of holophyly, whereas a heterocladic pattern only indicates a lack of holophyly: it is not then possible to formally decide between a real situation of paraphyly or polyphyly.
Translated: para- and polyphyletic groups have the same shape on a tree, while monophyletic groups are significantly different from both. Yes. That is one of the cladist arguments for accepting only the latter, and for considering para- and monophyletic so different that one shouldn't lump them into a term like 'monophyletic' sensu Aubert.

I must admit that I got somewhat lost around the definitions of stem group, crown group and basal group. Stem and crown appear to be used in the same way as by everybody else, although there is a strange excurs arguing that because people find it useful to have a word for the branch between the lineage split that created a clade and the first surviving lineage split in the clade we should formally accept paraphyletic taxa. This does not follow, to say the least. But 'basal group' seems to be defined as all species of the clade that have already produced other descendant species. As Aubert believes that species can split off other species and still stay the same species (see Composite Species Concept) and thus be terminals themselves, the utility of this term is unclear to me.

Pages 26-27 reintroduce another previously seen paraphylist attempt at defining oneself to victory: Cladists do not classify, they only arrange, because a classification is about affinity, and of course the only meaning of affinity that Aubert accepts is phenetic similarity. Being related is not an affinity, apparently. Also, classifications should contain "similar objects". Like species, for example, which just happen to be the basal units of phylogenetic systematics?

The definitions peter out with 'cladogram', and are followed by a more structured discussion of history and philosophy of science.

So, are Aubert's definitions preferable to the currently accepted ones?

The real question is then, if the definitions provided by Aubert are supposed to be better, better in what sense? Explicitly the abstract claims:

First, that the current terminology "prevents proper communication between the proponents of either side". This is a red herring, because any set of definitions facilitates communications as soon as it is universally accepted. As the people using Haeckel's meaning of monophyly, for example, are clearly in the minority, the best course of action for somebody genuinely concerned about communication would be to tell them to use Hennig's meaning instead.

Second, that "consequently, the research in phylogenetics is globally erratic and the taxonomic classification is highly unstable." I have already given the only possible answer: Instability arises necessarily from progress in our scientific understanding of the diversity of life, regardless of what terminology we use. Classifications changed before cladism, only there was no clear criterion to settle the issue once enough data are in.

The rest of the paper supplies two additional claims, sometimes implicitly.

Third, that Aubert's definitions are to be preferred for 'morphosemantic' reasons. It is true that monophyletic is perhaps not ideal from that perspective compared to holophyletic, because the latter does stress the inclusion of all descendants of the common ancestor.

However, at least in my eyes such arguments are handily trumped by the practical consideration of minimising the confusion and disruption that would be caused by changing a widely accepted meaning. It could also be pointed out that Aubert himself is not consistent in that regard: hetero- means different, so to use heterophyletic as a synonym for what is now called non-monophyletic (~non-holophyletic sensu Aubert) seems odd from a 'morphosemantic' perspective. By his own logic, it should probably be a synonym for polyphyletic.

Fourth, that the new definitions and terms capture something or clarify or add precision to something in a way that had previously been overlooked. This and the first one (to facilitate communication) are also what I personally would consider to be the two legitimate reasons for any attempt at altering a terminology.

As should be clear from the above, I don't think they do. Several of them are clearly instances of circular argumentation, like lineage or ancestral group; more on that perhaps in subsequent posts dealing with the supposed impossibility of phylogenetic classifications etc. Others lump very different biological realities into one term, such as 'monophyletic' sensu Aubert, so they do the opposite of capturing something about nature as it is. Yet others would only lead to more confusion, such as again redefining 'monophyletic' or the new words for describing group shapes in synchronous classifications where others already exist. Many simply appear to be irrelevant.

Most importantly, however, it is all besides the point. No matter how much definitions are shuffled around, the real questions are on the lines of what classification would be most predictive, most useful, most natural, most objective, and so on. The real question is not whether I can write down "rock is a kind of cheese" and get it published somewhere, but whether I can demonstrate that the moon is indeed made from milk products.

As far as I can tell, there is essentially one actual argument in favour of paraphyletic taxa in the 54 page paper (spoiler: it is the same as Brummitt's). Of course, one argument would be enough if it was sound. But enough for now, this has got long enough.


  1. Hi Alexander,
    The first part of your post seems to be a trial of intent, i.e. an ad hominem fallacy. The entire math I use can be understood by a 17-year-old pupil, so there is no intimidation for a senior researcher. Moreover, it is perfectly impossible to study the algebraic properties of a mathematical object without mathematically defining it. So, your suggestion that I should have used only plain language definitions is at best an ad populum fallacy. The fact that I warn myself against empty precision is not a case against precision in absolute. The aim of my analysis of terminology is indeed to assess the consistency (or nonemptiness) of the associated concepts.

    The fact of calling “paraphylists” evolutionary systematists is quite provocative. Evolutionary systematists are not obsessed with paraphyly; but cladists are really obsessed with holophyly. Cladists could be called holophylists, whereas evolutionary systematists would be better called monophylists.

    So now, concentrating on the more relevant parts of your post. The word lineage can be understood at an individual level as well as at a populational level. My definition fit both. The way I define an ancestor has absolutely no consequence on our debates. You may be unfamiliar with math papers, but it is a very common trick used by many. Kwok (2011) uses the same, you should read it.

    Again, your worries against my definition of a group is a non-issue. A set exists as long as its elements exist. The cladist usage of this verb (as well as quotes…), like “fish don’t exist” is only propaganda. The set of my cat and my keys in my pocket exists because both exist. Relevancy and existence are clearly distinct concepts.

    Moreover, a group can be ancestral to another without all the members of the former being ancestral the latter. Just like you can be the parent of a child without all your cells being ancestral to the zygote. In the limit case, the colony of cells you are calling “me” becomes a paraphyletic group when you have children.

    Concerning chloroplasts, you don’t seem to understand that in order to make cyanobacteria truly holophyletic you must include all plants. Plants didn’t arise through gene transfer, but through complete lineage merging.

    1. Okay, maybe it is just me, but I did not understand several of your symbolic definitions, and others only after a lengthy forward and backward and "wait, what was g' again?" But I suspect that all of them could be expressed with single sentences or simple graphs, so why not do it like that? Nor is exhorting somebody to write in an accessible way an ad populum fallacy, not least because it does not suggest that you are wrong.

      Paraphylists/holophylists: I disagree. Pragmatically, however, 'evolutionary' systematist is not only a misnomer in my eyes but also a mouthful, so I wanted something as short as cladist. Gradist perhaps? Also, saying that cladists are obsessed with monophyly is like saying scientists are obsessed with the scientific method.

      Nobody doubts that fish exist, the point is just that some of them evolved to live on land (as opposed to tetrapods poofing into existence ex nihilo). In addition, there is no reason not to use fish as a paraphyletic category outside of the formal systematic classification of life. Again, have you ever run into a cladist who told you not to say "tree" because that group is polyphyletic?

      For the ancestry issue, please see also my next post.

      No, I only need to include the chloroplasts to make cyanobacteria monophyletic. Then again, I am not working at that level.

    2. The shorthand word for evolution(ary systemat)ist is simply evolutionist, since in evolutionists eyes cladism does reflect evolution but distorts it. But I guess this is also a misnomer to you. "Gradist" is misleading because evolutionists recognize taxa that are not grades (see Cavalier-Smith 1998, figure 3). Gradism apply only to Lamarck and Haeckel (see my table 3). A neutral term that would satisfy both schools may be "synthetist", as suggested by Holynski in his 2015 unpublished paper, and many others before him.

      I disagree that holophyly has anything to do with scientific method in taxonomy (as opposed to the usefulness of this property for infering phylogeny), it is just an artificial convention to me.

      For the ancestry issue I will comment your next post latter. But again I disagree that chloroplasts alone are the descendants of cyanobacteria. Chloroplasts aren't organisms, the whole plant cell should considered as a chimera between a protozoan cell and a bacterial cell. The origination of plants is really different from kleptoplasty.

  2. Your treatment of my utilitarian argument is quite unfair. Evolutionists need the concept of monophyly sensu Haeckel to express their ideas. But you say that since the concept of monophyly sensu evolutionists is wrong, there shall be no word to express it, and this is an intended feature. So “you are wrong, now shut up!” Maybe I should have called it the anti-authoritarian argument. This kind of hijacking of language so as to avoid opponents to make their point makes me think more of Orwell’s Newspeak than a fair scientific debate. Secondly, the fact that “clan” was coined to fill this gap doesn’t undermine my argument since “clan” does not fit in X-phyletic series of words. Your suggestion that evolutionists should coin a new word themselves is again provocative. Ok, polyphyletic means “many origins”, and now I would like to coin a new word meaning “one origin”, let see how we can say “one” in Greek… Ah yes, it’s “mono-” (sarcasm) … Furthermore, several authors have used the words diphyletic and triphyletic for polyphylies of degree 2 and 3 respectively.

    You recognize yourself that holophyletic is a better word for your concept of “monophyly”. So just use it. As monophyly is not a useful concept to you, you won’t use it, so there will be no ambiguity in cladist papers. Holophyly is recognized as a non-ambiguous synonym, so there is no reason not to use it, besides political (authoritarian) reasons. Moreover, early cladists didn’t wonder so much about disrupting communication when they hijacked “monophyly” from its original meaning. On your side, you may be right that heterophyletic is not morphosemantically ideal, however this is really a side issue. I didn’t coined it (Zander did), merophyletic could have been better but “mero” and “hetero” have quite the same interpretation, whereas “holo” and “mono” have clearly opposite meaning. However, if you really want to correct this, it is really easy to do.

    You seem to overlook that systematics is not only a biological science, but also a classificatory science. As such, it should use a precise classificatory terminology. For example, holoclady and holophyly are really different concepts, the former being based on set-theory and the latter on graph-theory. Their logical and biological properties are thus quite different, and your arguments against the “composite species concept” relies entirely on this unrealistic conflation. Furthermore, you do not seem to have notice that I have argued that the distinction between synchronous and diachronous classification is irrelevant. Same remark concerning “classify” and “arrange”, and other classificatory terms. Some cladists have recognized that their “phylogenetic classification” should not be called a “classification”, but rather an arrangement or a systematization (see Griffith).

    As a last point, I will simply point out that you can make scientific progress in understanding the relationships between things without changing the names of these things. Instability in taxonomy does not arise from progress, but from cladist dogma against paraphyly. This is again propaganda to say the contrary. Haeckel already knew 150 years ago that reptiles were paraphyletic. Saying today that “reptiles don’t exist” is not a progress in knowledge. Furthermore, evolutionists do take into account phylogenetic results in order to make a better classification.

    1. At least in my eyes this is not "there shall be no word to express your disagreement" but rather on the lines of "elan vital is not a useful concept, so just drop it". Wanting a word ending in -phyletic is not quite the same thing as claiming that there is no word.

      Yes, of course I was being a bit snarky, sorry. But it is astonishing how many new terms you have defined in your paper alone. As I wrote, for me the avoidance of confusion trumps etymology; there is nothing authoritarian about this. As for cladists causing confusion, I was not around in the 1960ies, so I may be missing something, but my feeling is that the word monophyletic just didn't play the same crucial role before Hennig. Seriously, who still cares about Haeckel, except perhaps a few creationists who are obsessed with showing that he supposedly manipulated his drawings? Yes, the etymology of heterophyly is a side issue, and so are all these etymological hair-splittings.

      I think that you may be taking graph theory, set theory and words like classify too seriously, and biology not seriously enough. Systematics is a biological science full stop. We can attempt to build a system (or whatever we want to call it) that reflects biological reality, or we can insist on strict Linnean ranks and graph theory. I know where I stand on this; the latter approach looks a bit too much like trying to fit the square peg of reality into the round hole of an ideal. There will be splinters.

      You may have misunderstood my intent. The first point was that systematics should reflect our understanding, not that wrong systematics impedes progress - although coincidentally I believe that too! As for instability, did you just write "instability in taxonomy [arises] from cladist dogma against paraphyly" AND "evolutionists do take into account phylogenetic results in order to make a better classification"? I think this is what trying to have it both ways looks like.

      No cladist doubts that reptiles exist, only some of them evolved to be... oh, I think we had that already.

    2. The case of "élan vital" is quite different from that of "monophyly". Even if the concept is nonsensical to us, nobody tried to redefined this words in order to prevent vitalists to express their ideas.

      Wanting to restore a hijacked term, central to the framework of synthetists, is quite legitimate (to say the least). I suspect that this will never stop as long as synthetists exist (and I am not very old). So, why not considering to say "holophyly"? If not for political reasons?

      I disagree that systematics in only a biological science. This is like saying that physics is only a physical science and that using math is following an ideal leading us far from reality. Classificatory science is a tool. In fact I think that this kind of ideal is precisely the holophyly principle. Sister-group analysis is only an indirect evidence to infer ancestor-descendant relationship. Sister-group relationship is unreal while ancestor-descendant is a real one. So classifying according to the former is artificial and classifying according to the latter is natural. Linnean ranks are not an ideal, they capture an empirical reality which is the hierarchy of adaptive zones, i.e. stasis and revolutions (dynamics and kinetics of evolution).

      The goal of evolutionary systematics

    3. The shorthand word for evolution(ary systemat)ist is simply evolutionist

      Evolutionist appears to be a creationist slur that implies evolutionary biology is not a science but a political movement, like they are. But again, in my eyes you worry too much about words and too little about biology.

      Chloroplasts aren't organisms, the whole plant cell should considered as a chimera between a protozoan cell and a bacterial cell.

      This is a complete side issue, but we will have to agree to disagree. As far as I am concerned, we do not classify genes but organisms, and we do not classify by similarity but by descent. The chloroplasts are descended in a direct line, generation for unbroken generation, from a single cyanobacterium that was originally engulfed but not digested. The rest of the cell is descended, ancestor to descendant generation for unbroken generation, from the eukaryote who engulfed that first chloroplast, notwithstanding that it has taken over many of the genes originally residing in the latter.

      So, why not considering to say "holophyly"?

      As I have written repeatedly, avoiding to create in reality the confusion that currently only exists in the imagination of a small minority seems more important to me than etymological hair-splitting.

      I just did a quick GS search. It retrieves 1,030 hits for holophyletic, which would presumably include papers arguing against its use. And interestingly, GS suggests "did you mean: polyphyletic", implying that the search engine is not sure it is a real word. On the other hand, there are "about 94,000" hits for monophyletic. So yes, we are talking an approximately 1% issue here, which more or less fits my expectations. If 1% of people started arguing that we should change the definition of the word cheese to include moon rock I would also tend to disagree, for similar reasons.

      I disagree that holophyly has anything to do with scientific method in taxonomy (as opposed to the usefulness of this property for infering phylogeny), it is just an artificial convention to me.

      Monophyly sensu Hennig is not an artificial convention, it is the systematics counterpart of the old discussion about whether non-Greek, for example, is a useful category on equal footing with Greek. Paraphyletic groups are equivalent because they are defined based on arbitrarily excluding a subgroup, on including items only for lacking a certain affinity, and thus artificial.

      Sister-group relationship is unreal while ancestor-descendant is a real one.

      If common descent is assumed to be true, then sister group relationships are real. They are real even in your abstract graphs; you are only confused about what to do with the ancestral species, because you treat it as a static diamond on paper that has to go into all Linnean ranks.

      Does it go into the left descendant group or into the right one? The one and a half biologically realistic answers are: neither or, in a certain sense, both. Because the ancestor is not (only) one of its own descendants it doesn't belong into either of the descendant groups. But it has become both descendant groups. So really the species that was once the common ancestor of all birds is right now all extant bird species, not merely another diamond in the circle you would label "birds".


    4. This is like saying that physics is only a physical science and that using math is following an ideal leading us far from reality.

      I am not a physicist, but as far as I understand the aim of physicists is to choose the model, description or formula that best approximates reality. They do not appear to start with a mathematical abstraction and then insist that nature must be hammered into it whether it fits or not. Nor do they generally insist that a colleague searching for a better fitting model is attempting the "formally impossible" merely because she is willing to move beyond the traditional model from 1753.

      Linnean ranks are not an ideal, they capture an empirical reality which is the hierarchy of adaptive zones, i.e. stasis and revolutions (dynamics and kinetics of evolution).

      Linnean ranks were invented in ignorance of common descent.

      You sometimes read as if you are a saltationist. As far as I know, there is no evidence whatsoever for the sudden revolutions that you imply have happened. How would that even work from the perspectives of population genetics, genomics, or developmental biology? We only have the illusion of saltations due to an incomplete fossil record.

      But well, we will not be able to reach agreement here. You start by assuming that taxa should be based on phenetic similarity and argue from there, I start from the assumption that the job of a systematist has always been to figure out what characters are truly indicative of relatedness (instead of classifying all butterfly larvae into a different class than the respective adults, for example) and then merely apply that approach consistently. It is unfortunately likely that we will only go in circles from there.

    5. We have to agree that we disagree, I think you don't worry about words (and thus concepts) enough, and you think I worry too much.

      However, using "holophyly" instead of "monophyly" is not (at all) the same thing as redefining a word, as you insinuate with your rock/cheese analogy. You can just consider they are synonyms and then use the non-ambiguous one. As a cladist, you don't need a word for "holophyly+paraphyly", right? So again, there are no reason not to use the neutral synonym. Your argumentum ad Googlum is irrelevant.

      Your Greek/non-Greek analogy is also irrelevant. It is just the same propaganda, straw man argument, I heard so many times. Of course, we don't classify the all life into bird and non-bird. Furthermore the word "lacking" is misleading. "Not being A" is the same as "being non-A". It is the same fallacy as the Popperian opposition falsificationism/verificationism.

      I argue that the Hennigian holophyly principle is "the mathematical abstraction [that cladists coined and] then insist[ed] that nature must be hammered into it whether it fits or not."

      Linnean ranks were surely invented in ignorance of common descent, but they nevertheless captured an empirical fact. This fact (hierarchy of the living world) directly inspired the theory of evolution to Darwin.

      Finally, can't you make a distinction between saltationism and punctualism? Accelerated evolution (with only gradual micromutation) in short periods of time and long stasis is not at all a problem for population genetics, genomics, or developmental biology. I disagree with your "incomplete fossil record" argument, it has been falsified in many cases.

    6. If my concern is with clear communication, then stats on how many people use the various terms are the ONLY thing that is relevant.

      Many paraphylists do want to classify dinosaurs into avian and non-avian ones, for example. Which is even more curious because there we really have all intermediate fossils, making it quite impossible to draw a convincing line.

      I have no idea what empirical fact the Linnean rank order captures, for example. How do you test empirically and objectively whether a group is an order, as opposed to a family?

      Frankly I am not sure that you make the distinction. Punctuated equilibrium is a variant of gradualism, and I am agnostic on whether PE is correct in the first place.

      More importantly, this discussion is muddled because you would actually need saltationism to be be true to make the arguments you are making, to justify 'evolutionary' classification. PE doesn't cut it. If evolution is gradual, via changes of allele frequencies in populations, there have never been the long branches or gaps in variation required to cleave off paraphyletic residues in an even only somewhat objective manner.

      The only way to falsify the argument I actually made would be if you could demonstrate that paraphylists have never argued for recognising paraphyletic taxa based on long branches, gaps in variation, and "but they look so different". It is an argument about what people argue, not about the fossil record itself.

  3. I disagree that if your concern is "clear communication, then stats on how many people use the various terms are the ONLY thing that is relevant". It is a political view. If you are a scientist, clear communication implies proper terminology, rigorous concepts and a fair way of rebutting your opponents. Again, I see your attachment of using "monophyly" instead of holophyly as an authoritarian issue.

    Ranks are relative, not absolute, so defining what is a family or an order in absolute is of course nonsensical, as everyone knows.

    I know punctualism is a variant of gradualism, I even said it in my very paper.

    So, no, I don't need saltationism.

    Of course there are no real gaps and long branches are full of transitional fossils. But it is irrelevant to the fact that there are stasis and revolutions. Revolutions don't need to be instantaneous. A revolution is an acceleration of history, not a point in time.

    So how to cleave off paraphyletic residue in an objective manner? To do so, the better way is to search in the fossil record an acceleration of evolution followed by an adaptive radiation. The cut can be made at the key innovation, i.e. the one directly responsible for the burst. Interestingly, the case of birds matches exactly this scenario, see for example Brusatte et al. (2014) Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution across the Dinosaur-Bird Transition. Patrocladistic classification and other methods can be considered as heuristics to discover these leaps.

    1. I see your attachment of using "monophyly" instead of holophyly as an authoritarian issue.

      Well, then feel free to go on seeing it as that if you can't accept my real rationale. The rebuttal still took place in the 1970ies and used biological instead of linguistic arguments, as it should.

      Ranks: But there are really only two differences that matter between something like the PhyloCode and the Linnean system, that the latter has got explicit ranks and that it originally required an organism to be assigned at every rank, in the case of fossils even the ones that only came into existence after the fossil organism existed. You have just implied that the first is irrelevant, and the second is where its pre-evolutionary character shows most strongly. If you praise the Linnean system merely for reflecting common descent by being nested, well, so does a cladistic classification.

      How to cleave: I am afraid you do not understand. If you want to have a half-way objective and testable criterion for delimitation of paraphyletic groups you need abrupt gaps in variation, not merely variation in rates of changes. (And even then it isn't very universal and reproducible: a gap in what traits, and why those?) You have just acknowledged that there are no such gaps, that there is just a gradient of transitional forms. By definition such a gradient cannot be cleaved in an objective way, because it is a gradient. But then you fall back into saying "leaps", which you just ruled out, and thus your language itself becomes saltationist! That way it really comes across as wanting to have it both ways.

      I am not sure your reference to adaptive radiations makes much sense either, both because you may be confusing it with high diversification rates and because I fail to see how either a nested clade having a higher net diversification rate, or the nested clade having evolved into several novel niches, or the synapomorphy of the nested clade being a key adaptation would justify formally recognising the grade under it. This is just what I am saying: you point towards what makes the Greeks special to argue that the non-Greeks are a meaningful group. That argument has the wrong focus. Having established something as not-being-A is simply no guarantee that it makes sense to call it B, only that we can call it not-A.

      I have read Stuessy's patrocladism paper and a follow-up. In effect the method clusters by distance on the phylogenetic tree. There are many problems, not least that it appears impossible to find any theoretical justification for this approach, but the relevant one for the purposes of this comment thread is that IRL patristic distances do not exist, only the illusion thereof due to our current ignorance of the extinct intermediates. As you acknowledged yourself just now. 'Evolutionary' systematics nearly always reduces to the long branch illusion.

      The biggest irony here is, however, that it is the pro-paraphyly side that constantly claims cladists ignore anagenesis and ancestors, and then the anagensis and ancestors that must have happened and existed along a branch conveniently go out of the window when discussing how to reproducibly and objectively circumscribe paraphyletic taxa.

  4. You persist in not understanding that evolutionary systematists classify according to the PROCESS of evolution. Your "long branch" argument is only about PATTERN. So yes, it is completely irrelevant to me and to any evolutionist. Saying that patristic distance doesn't exist is nonsensical, there are simply more or less intermediate species along the different branches. So again, we don't need abrupt gaps. A leap is not a gap. Gaps are discrete whereas leaps are continuums. Not understanding this is what I call metaphysical thinking, the contrary being dialectical thinking. Or should I find a German word to express this idea? Aufhebung?

    1. If you appreciated the process of evolution, you would not treat the ancestral species as a diamond on paper that needs to go into one of its two descendant groups, or conflate something like mother-daughter with fish-tetrapods.

      If a leap is a continuum, you cannot objectively cleave it into two same-level groups. Curious how you can see that when you claim that mother-daughter is the same as fish-tetrapods but not when having to decide whether Tiktaalik is a fish or not.

  5. I do not conflate mother-daughter with fish-tetrapod, but I have shown that the topological properties of the former are inherited to the latter, simply by zooming out.

    Why couldn't I cleave a continuum into two same-level groups? The continuum is not homogeneous, so I can perfectly decide by using heterogeneities. So Tiktaalik is a fish, since the rapid burst of tetrapod speciation happened just after. When a revolution happen there is always a before and an after. So first of all, there is no problem in contrasting before/after, i.e. paraphyly/autophyly. Secondly, the revolutionary period is necessarily fuzzy, so there is always a small degree of subjectivity when deciding exactly where to cut. But the fuzzy period itself can be clearly and objectively determined and it is not a problem to acknowledge reality, historians have the same kind of dilemma when cutting historical periods from the continuum of history. Finally, in practice it is very rare to have a fossil that we cannot decide if it is before or after the revolution, usually a key innovation can be causally linked to the adaptive radiation and so serves as an objective cut (not to mention when we don't have any fossil of that period).

    1. Okay, I must admit your approach is a new one to me. Usually proponents of paraphyletic taxa searching for an objective criterion go for the long branch fallacy. But you say, fine, there is no long branch, but along a branch there can be a shift in diversification rates that justifies the formal recognition ... of the grade that did not undergo the shift. Yes, the problem is once more the same: the Greeks have trait X, and therefore all the non-Greeks are a valid group equivalent to the Greeks.

    2. I don't think my approach to be particularly an original one. If you have read Zander, Hörandl, Stuessy and many others, they say quite the same things, although each one perhaps with their own words. The gap/long branch fallacy was only a pitfall for 1960ies evolutionary systematists.

      Your non-Greek/Greek analogy is nonsensical to me and I don't understand how it can convince someone. Evolution is all about transformation, i.e. A becoming non-A which we could then name B. And then you reproaches us to recognize A because it is a non-B ! This is partly why evolutionists say that cladists ignore evolution, i.e. evolutionary process. Representing evolution by a pattern only is to us a misrepresentation.

    3. No, I have read them, and this thing with the shifts in diversification rates appears original to you. For example, Stuessy's output in this context is explicitly about using the long branches, that is what patrocladism is all about.

      Evolutionary theory has speciation events, mutation, selection, drift. None of that is a problem for cladism. On the other hand, I do not know that evolution is about transformation from one genus into another, for example. It seems silent on the genusification events that you would need to even talk about paraphyletic genera in any meaningful way.

    4. I think you have misinterpreted them. Shifts in the rate of evolution (i.e., process) results in an apparent long branch on the pattern of the cladogram. It is understandable since it is correlated with a high rate of extinction. So it is perfectly defensible to treat this pattern as a data in order to infer the process which caused it.

      Not all evolutionary theories are silent about genera arising from other genera. It is predicted for example by punctuated equilibrium theory. See Zander's book (2013) "A Framework for Post-Phylogenetic Systematics".

    5. That would have to be quite the shift in rates! So you really believe that one species produces, in the blink of an eye, another that differs in five major traits, without any intermediates breaking your classification up? That is saltationism.

      I am seriously starting to think that no 'evolutionary' systematist understands punctuated equilibrium. Its claim is that changes happen at speciation events, and that species are static between speciation events. Its claim is NOT that changes at speciation events are saltationist. Nor is it that most speciation events produce little change and some of them are saltationist, although that is what you would need to be true.

      And who knows if either Gould's PE or your misinterpretation of it are correct; people generally seem to find Brownian Motion models of rate shifts to be a good fit to the data.

    6. Are you serious? Or, are you trying to straw-man my claims? Where did you read that I claim there are no intermediates or that only one speciation event is needed for the evolution of 5 major traits? "Blink of an eye" can be 1 Ma in the geological times, you can have 10 speciations events in one branch and zero in the sister one. So yes, if these 10 intermediate species remain unsampled you will see a long branch on your cladogram and you will be able to hypothesize there was a high rate of evolution (= revolution) between two stasis. I don't need saltation to draw this scenario. Besides, brownian motion models only fit stasis periods.

    7. We have been through this before. I thought I understood you, but seems I was mistaken.

      Do you believe that there were 10 intermediate species? Then you do not and cannot possibly have an objective cleavage point to recognise the paraphyletic reside as separate at the same level as the nested clade.

      Do you argue that you have such an objective cleavage point because there is a long branch? Then you pretend that 9 anagenetic species didn't exist, and you are a saltationist.

      Unless I severely misunderstand, you are trying to have it both ways after all.

      Brownian motion models appear to fit character evolution in many real life phylogenies. Look into the contemporary literature on rate shifts and see if you can even find PunctEqu models implemented in Mesquite, BAMM or whatever. Nobody who works with real data on the ground seems to see a need for them.

      Also, you must have a non-standard understanding of the term 'stasis' if you think that a model of character evolution, that is non-stasis, fits it.

    8. Yes, you severely misunderstand.

      In all cases there are 10 intermediate species.

      First subcase, the fossil record is incomplete. So you don't know the intermediate species and then you have a long branch on your cladogram. The long branch is thus an objective cleavage.

      Second subcase, the fossil record is complete. So you can witness all the intermediate species. The adaptive radiation happens only when this lineage enters the new ecological niche. You don't see a "long branch" on your cladogram but a shift in speciation rate when the key innovation occurs. So this key synapomorphy is an objective cleavage point. If you can't clearly identify the key innovation you can still cut just before the burst. Hence, tetrapodomorph fishs are still fishs.

      As for stasis being "non-evolution", you should read Cavalier-Smith (2006) "Cell evolution and Earth history: stasis and revolution". Stasis are like revolutions, they can happen at different relative levels (hence ranks).

    9. In the first case, you are essentially saying that your approach to classification would have to rely on being lucky enough to have a sufficient degree of extinction and an incomplete fossil record. Hardly a method that we could call universally applicable.

      In the second case, I agree completely that a synapomorphy is good for defining a group, the tetrapods. But you are still trying to define another group, the fishes, based on not having that synapomorphy. Again, football players versus people who don't play football.

      You don't understand why that is a problem, I know, but many people understand what is wrong with the second 'group', and it is one of the arguments for phylogenetic systematics that really matter.

      Thanks for clarifying that we are indeed using different meanings of stasis.

    10. Whether one should define paraphyletic groups or not is a different issue than whether one can define them or not.

      On the former issue we can agree that we disagree, but your justification does not hold. It is an irrelevant comparison. You try to show that a group nominally defined by not having a certain property is always non-cohesive (hence nominalism). Your argument is always just a dubious example, like Greek/non-Greek or football-players/non-football-players. By the way, it is not because many people are convinced by this fallacy that it is not a fallacy.

      The point of realism is that the cohesiveness of group cannot be predicted from the manner it was nominally defined. These are completely independent issues. Inside the group of Greeks I could define subgroups males and non-males. Then yes non-males is a cohesive group. On a football field during a match between France and Germany, I could define groups French and non-French, obviously both of them being cohesive. But these are just examples, any analogy is always dubious is some extent. Evolutionnists address the cohesiveness of groups with biological reasoning, i.e. common evolutionary behaviour, ecological niche, etc.

    11. You have carefully chosen examples that are analogous to sister clades on the tree of life, in other words cases where you and a cladist would be in perfect agreement.

      Again, I do not particularly care about being sorted into a nominalist or realist box. If you tell me that believing the sky is blue makes me a zorkist that in itself wouldn't change my opinion either.

      I do not understand what you mean with cohesiveness of groups if not superficial phenetic similarity; evolutionary biology knows no mechanism by which even two closely related species necessarily have to show "common evolutionary behaviour", whatever that even means. They have diverged, and they may not even be on the same continent any more.

      Ecological niche? We have several ecology niche based classifications for that, if you can even define what you mean. Do tuna and coelacanths have the same ecological niche just because they both swim around in the ocean? Because if you go fine scale enough you can justify a new order at every speciation event that is driven by a shift in some interaction with the environment.

  6. For the moment, let's set aside the dubious merits of patrocladistic methods and Linnean ranks. The ranking of paraphyletic residues is a separate question from whether parent grade / daughter clade is a useful way to think about evolution. I think it can be.

    For any living species, a nested set of clades represents an increasingly general categorization as well an ancestor-descendant lineage. The ancestral Hyla is descended from the ancestral frog is descended from the ancestral lissamphibian; the ancestral Passer is descended from the ancestral bird is descended from the ancestral amniote; both are descended from the ancestral tetrapod. But if I want to talk about some fossil tetrapods that illustrate that divergence, I'll need to remove clades in order to be more specific. No, not just any tetrapod, a non-amniote non-lissamphibian tetrapod ("labirynthodont?").

    In most cases, yes, clades are more informative than grades. While they circumscribe the same extant species, the difference between the old paraphytic "Amphibia" and the crown clade Lissamphibia is about 100 million years of evolution and a long list of apomorphies, some of which can't be inferred from fossils. In other cases, the differences are minimal to non-existent, depending on the preferred phylogenetic hypothesis (gymnosperms). A strongly supported grade (i.e. non-avialan maniraptorans) is better than a weakly supported potential side branch (deinonychosaurids) if you're studying bird evolution and would like stable names.

    The important thing is having convenient and unambiguous words available to describe groups of evolutionary, ecological, or economic interest and make valid inferences about their characters and evolutionary relationships.

    1. I am not really sure what you are arguing here. The concern of a cladist would be that paraphyletic groups mislead about evolutionary relationships and character evolution. For groups of ecological and economic interest, non-phylogenetic classifications containing categories such as 'predator' or 'noxious weed' might indeed be more useful.

    2. I just don't see what's so unscientific or misleading about paraphyletic groups provided
      1. they can be distinguished from clades, using a typographic convention such as lowercase, scare quotes, or an asterisk (amphibian, "amphibian", Class Amphibia*)
      2. they can be unambiguously defined relative to more and less inclusive clades ("amphibian" = non-amniote tetrapod)

      You identify a fallacy associated with grade->clade thinking in the next post in your series...
      For example, paraphylists would claim that the whole paraphyletic 'group' of bony fish is ancestral to the tetrapod land animals. But are, say, New Caledonian Thorny Seahorses actually ancestral to us? Of course not; that species only originated hundreds of millions of years after the tetrapods originated, so how can it be an ancestor of tetrapods?
      ...but many people misinterpret more basal branches of a cladogram in the same way.

      In paleontology, paraphyletic groups seem unavoidable. There are 115,000 google hits and 578 Google Scholar hits for "non-avian dinosaur." Nobody uses a clade like Reptiliomorpha except to imply that a fossil is not an amniote.

      I also don't see the value of appropriating the name of a taxon traditionally understood to be paraphyletic. "Birds are sauropsid amniotes" is much less ambiguous than "birds are reptiles."

    3. I must admit that the finer points of vertebrate systematics are not my forte. Still it should be obvious that there is no clear line to be drawn between non-avian dinosaurs and birds. If you had been born in 70 Myr BCE, you would laugh everybody who suggested to treat those groups as separate out of the room, because you would not be able to see any gap in variation with all the feathered dinosaurs around you.

      It is only due to extinction and ignorance that the scientists who came before us ever made that mistake. And doesn't treating them as separate just perpetuate the caricature of dinosaurs as all being scaly monstrous lizards?

      Another example: When discussing convergent evolution versus contingency, I once came across the argument that many vertebrate groups did not show any increase in brain capacity and intelligence, so there was no convergence. Look at the dinosaurs, for example! (Can't find it again, but I seem to remember there is even a Gould quote with the same content.) I found that unbelievable at the moment; apparently the person who advanced the argument was unaware that corvids and parrots are brainy dinosaurs.

      That is precisely what a misleading classification looks like.