Did you say Evolution doesn't teach man evolved from ape?

Cirbryn · Jul 31, 2006

Note: this post, as well as the one immediately preceding, are in response to post 357. The tree of brown bear mitochondrial DNA discussed herein is reproduced in post 355. I realize the quote boxes in this post are a bit messed up. I've tried taking out the internal close-quotes but the system keeps putting them back.

Cirbryn said:
Other such characteristics might reflect adaptations for particular niches or environments, as with cetaceans, or polar bears, or mosasaurs; or simply reflect body plans that were important phylogenetic starting points, such as the morganucodontids. How would a cladist identify the morganucodontids?

Aron-Ra said:

As Cynodontids, if not simply as therians. But Morganuconodonts may work just as well when you subtract them out of the parent group.

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Aron-Ra said:

"Although they are one of the earliest groups of mammals, its not possible to say whether they went entirely extinct or whether they are in fact the ancestors of any of the other, later groups of mammals." --BBC; Walking with Prehistoric Beasts

Just to clarify for you once again, if it appears that our lineage is rooted in that one, then we are Morgauonodonts. However, if I speak of them with no further clarifiers, I will likely be referring to the stem rather than the whole of the clade. The reason is as SLP explained; the amount of information. If I'm speaking of more modern forms, I can identify them more precisely by saying 'Eutherian' than simply 'Therians' alone.

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I think this merely emphasizes my point that the cladistic crusade against paraphyletic groups leads to unnecessarily awkward naming conventions. The cladistic system allows us to identify a clade beginnng at any point in the lineage, but to avoid paraphyly any clade so identified must include the entire lineage from that point. So if the animals sharing specific characteristics and identified in the Linnaean system as Morganucodontidae occurred from point A to point B in the lineage leading to us, cladistics would allow us to name a clade going from point A to us, and one from point B to us, but not a group going from point A to point B. You are instead forced to refer to them as cynodonts (which is hardly helpful since cynodonts, by cladistic standards, would include the entire lineage starting well before the morganucodonts), or else to bring in unofficial conversational understandings that are unclear and that cant be employed in published papers. Under the Linnaean system, I can write that the morganucodont articular bone had not yet detached from the dentary. Under the cladistic system I cant say that; unless it turns out morganucodonts arent on the direct line leading to later mammals after all, in which case I can say it again.

Cirbryn said:
Are you even allowed to utter such a paraphyletic name as that?

Cirbryn said:
Aron-Ra said:

I can say anything I want, as long as it is understood what that means.

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No you cant under a cladistic system. Naming paraphyletic groups is verboten. Thats why youre having such a problem with the fact that monkeys is paraphyletic.

Cirbryn said:
Or how about the studies of brown bear mitochondrial DNA (recounted in Molecular Markers, Natural History and Evolution, John Avise, 2004) that found six geographically separate "Phylogroups" (intraspecific clades), one of which that of southeastern Alaska had DNA so similar to polar bears as to indicate polar bears were members of that group? So before the study there were brown bears and polar bears and after the study there are just brown brown bears and white brown bears?

Aron-Ra said:

What about them? If it were that polar bears emerged from within "brown" bears (as generic a name as one can have) then yes, polar bears would be brown bears that are white. Coincidentally, I also know a man named Green, but he's not. Once again, the characters don't matter in the least. Only the phylogeny is important.

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Since brown bears refers to a particular species, it is specific not generic, in both senses of both words. Brown bear is the English name for Ursus arctos. Youre saying that polar bears (Ursus maritimus) are members of Ursus arctos, by virtue of their phylogeny, and that the fact that maritimus and arctos no longer interbreed extensively in the wild makes no difference. (Interbreeding being one of those characters that according to you dont matter in the least). By this reasoning speciation could never occur. A daughter species would always remain the same species as its parent, and we would remain the same species as the first to ever appear on the planet.

Cirbryn said:
What if another study of some other genetic region indicates greater separation, or suggests the similarity of the first study was merely due to a limited instance of past interbreeding?

Aron-Ra said:

That was the explanation as I remember it. What of it?

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Your link only shows a single instance of current interbreeding involving a polar bear mother and a brown bear father. (Grizzlies are a subspecies of brown bear). It doesnt demonstrate interbreeding in the past at a level sufficient to explain the mtDNA sequences (which, for one thing, would have to have involved brown bear mothers and polar bear fathers). The point I was getting at is that by cladistic reasoning wed have to claim polar bears were the same species as brown bears based on the mtDNA sequences; but we might change our minds later if evidence of earlier limited interbreeding came up that could explain the sequences; but we might change our minds again after that if another gene showed similarities indicating descent from brown bears in addition to the interbreeding; etc. So not only does cladistics ignore speciation, it leaves species in a nomenclatural limbo where their names are subject to change from day to day.

Cirbryn · Aug 8, 2006

Note: the following is written in response to post 358.

Cirbryn said:
Humans are apes in the Linnaean system. Your college classes taught you otherwise because they were out of date. My 2001 college class on Mammology was not (on that point theres always something new). The book we used was Mammology 4th Ed by Vaughn, Ryan and Csaplewski. It presented mammals by order and family, with additional phylogenetic information thrown in. Hominidae was presented as a family, not a clade. Genera and species within the family were discussed.

Aron-Ra said:

That was the part that was out-of-date.

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It was not out of date. In fact it is still commonly used now. If you look up Mammals in Wikipedia you find the following:

Standardized textbook classification

A somewhat standardized classification system has been adopted by most current mammalogy classroom textbooks. The following taxonomy of extant and recently extinct mammals is from Vaughan et al. (2000).
Class Mammalia

Subclass Prototheria - monotremes: platypus and echidnas

Subclass Theria - live-bearing mammals

Infraclass Metatheria - marsupials

Infraclass Eutheria placentals

Note the reference to Linnaean ranks. Vaughan et al (2000) above is a reference to Mammalogy 4th edition the very book I was talking about. The subclasses and infraclasses discussed above are Linnaean taxa. The wiki article goes on to discuss an alternative classification system (McKenna/Bell) which was quickly accepted by paleontologists. The McKenna/Bell system also uses Linnaean ranks, but introduces some fine distinctions such as legions and sublegions (ranks which fall between classes and orders)that are likely to be glossed over by the layman. Thus both major textbook classification systems for mammals are Linnaean. Theres also the point I made earlier to consideringlily: Scientific classification of living organisms is almost exclusively Linnaean. Any field guide to plants or birds or mammals or anything else you are ever likely to see is Linnaean. Anything the Fish and Wildlife Service or the National Marine Fisheries Service or any state fish and game agency or National Heritage Foundation organization youd care to mention has published regarding any species, has related the taxonomy of that species in Linnaean terms. Any survey done by any biological consulting firm in the US has listed what theyve found in Linnaean terms. To suggest, as you do, that anyone accepting evolution must also reject Linnaean taxonomy, is completely and utterly ridiculous. And by Linnaean taxonomy, humans are not monkeys.

Cirbryn said:
Numerous websites take the same approach.

Aron-Ra said:

Many more take the opposite stance even when they would rather agree with you. In fact, I found only one (by Richard K. Brummitt) which acknowledged the phylogenetic alternative, and still argued from your perspective. However, even that one complained about a generation of "strong psychological pressures" promoting a "dogmatic obsession with monophyletic taxa", and that for the last fifty years, biologists have increasingly frequently made statements to the effect that the Linnaean system is incompatible with the evolutionary phylogenetic scheme, otherwise known as clades. This was a point he himself even agreed with, and he noted several others; zoologists Griffiths (1976)and de Queiroz & Gaither (1992) and (1994), and in botanical circles Cronquist (1987), Sosef (1997), and recently Cantino (1998, 1999; Cantino & al, 1999) in various papers promoting the Phylocode.
depts.washington.edu/phylo/LabMeetingReadings/ Week1/BrummittParaphyly2.pdf

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My goodness, what a delightful article to read! I expect I shall be thinking with a British accent for quite some time to come. And while Brummitt does acknowledge, as you say, the phylogenetic alternative, he makes clear that this alternative is the PhiloCode. He also doesnt bother to spend much time on it because he doesnt consider it likely to be widely adopted. As he says: If people feel the need to name clades, then it is difficult to argue that they should not do so, but they should not think it is going to displace traditional classification, particularly at the lower taxonomic ranks. It is not going to do so. ( p 31). The bulk of the article is spent attacking the practice, inspired by cladistics but not representative thereof, of requiring Linnaean ranks to be monophyletic. Such is not a phylogenetic alternative to the Linnaean system for two reasons: first, because it attempts to maintain and work within the Linnaean system, including its hierarchy of ranks; and second because, as Brummitt points out, it is simply not possible to make all Linnaean ranks monophyletic.

I think the first point has been the source of at least some of our confusion on this thread. You have apparently been assuming that the general push to recognize only monophyletic Linnaean taxa has indicated a general overthrow of the Linnaean system. Ive been assuming it does not, since the Linnaean taxa are maintained, and since monophyly in any particular taxon is not contrary to the Linnaean system. This has presumably been the basis of our disagreeement regarding the importance of moving the non-human great apes from Pongidae to Hominidae.

The second point that we cant make all Linnaean taxa monophyletic should be obvious. As Brummitt points out: Every monophyletic genus we recognise in the tree of life must have arisen from a single species in a different genus, which must be paraphyletic; every monophyletic family we recognise has been descended from one species which is referable to one genus which is in a different family, and all must be paraphyletic; and so on. This is the same thing Ive been pointing out regarding species: every speciation event establishes a paraphyletic taxon that of the parent species. This is so obvious that it is difficult to understand how anyone could argue against it. Brummitt, in his reserved British manner, says: If some still need some gentle convincing, I ought to remember to use the nice word counter-intuitive to describe the cladistic position. But I have to admit that in a recent publication (Brummitt, 1997) I actually used the word crazy instead, and on other occasions I have used the words absurd, daft, and nonsensical. And I am afraid I have referred to the arguments of those who vainly try to equate two completely incompatible systems as futile mental gymnastics.

There is an illuminating response to Brummitts paper in the same general archive by Nelson et al. (Thats Gareth Nelson, not L Aron Nelson). The response claims to answer Brummitts challenge to provide a phylogenetic tree, fully divided into Linnaean taxa without any being paraphyletic. The tree they offer, a variation on one published by Daniel Rosa in 1918, includes four genera (A, B, C and D) each of which descends from another genus that has gone extinct. Thats it. They apparently dont realize theyve just defined those extinct genera so that theyre paraphyletic groups that include the common ancestor but not all the descendants. Brummitt points this out politely in his response, but its difficult not to wonder how anyone could have missed such a simple point. The rest of Nelson et als arguments are little better. Where Brummitt posits a situation in which there are four related clades, only one of which is morphologically different from the others, they answer by changing the parameters such that the clade most closely related to the unusual one is itself morphologically distinct. They finally descend into blatant strawman attacks: For Brummitt, Evolution is paraphyly all the way: birds from nonbirds, being from nothingness, ex nihilo omnia. Brummitt never talked about being from nothingness, either in English or in Latin. The only reason its in there is to make birds from non-birds look odd by association. This is apparently the best that Brummitts opposition can muster. Im just astonished. Brummitt handles these critiques in his response with typical politeness and reserve, but I cant help but imagine whether he might have considered something more along the lines of the generalized reaction he relates towards the end of his original 2002 article: What is going on here? How does a normally reserved Englishman express his reactions to this to an American audience? Do I just say, Oh deary me, this does seem to be a little bit disturbing!? Do I look for slightly stronger words to attract your concern? Or do I borrow some phrases from your own sporting heroes who come over to Britain and take away all our silverware? What was it Mr. MacEnroe taught us? You can not be serious. Man, you can not be serious. This is the pits! The ball was on the line. The chalk flew up. Everyone here could see it. Just open your eyes.

And lest we forget about strawman attacks by people named Nelson, theres this claim of yours that Brummitt complained that for the last fifty years, biologists have increasingly frequently made statements to the effect that the Linnaean system is incompatible with the evolutionary phylogenetic scheme, otherwise known as clades. Brummitt never equated the evolutionary phylogenetic scheme with clades. He in fact went to some effort to point out the difference between phylogenetic trees (which show ancestors, for one thing) and clades (which dont). What youve done is to conflate one of Brummitts quotes of J. Woodger (The taxonomic system and the evolutionary phylogenetic scheme are quite different things doing quite different jobs, and only confusion will arise from identifying or mixing them) and a separate statement by Brummitt (our Linnaean system of classification is incompatible with a system which recognises only monophyletic taxa, otherwise known as clades.). Brummitts point is that Linnaean taxa cant all be made monophyletic, and that we shouldnt try to make them so. Evolutionary classification, he argues, paraphrazing Darwin and Mayr, depends on two factors, descent and modification. Attempts to make all taxa monophyletic emphasize the former at the expense of the latter, leading to impractical results. The Linnaean system, because of its paraphyly, is able to acknowledge modification while still allowing taxa to be mapped directly and easily to a phylogenetic tree.

Cirbryn · Aug 9, 2006

Cirbryn said:
A few slightly out of date courses in some Texas college does not demonstrate that the reorganization of Homididae and removal of Pongidae represent some kind of overthrow of the Linnaean system as it applies to apes. Nor does the fact that the intent of the reorganization was likely to make the great ape family monophyletic. Monophyly is allowed and often encouraged in the Linnaean system.

Aron-Ra said:

But only since the incorporation of phylogenetics, and only because of that, and for no other reason, by your own admission. Yet you still insist on paraphyly for monkeys. Why? What possible justification could you have for that exception?

And Brumitt's comments were written for a symposium in Washington D.C. where an exclusive choice between the Linnaean system vs. phylogenetic clades was being "seriously debated" before an audience of some 260 professional biologists. So it is hardly appropriate for you to pretend we're talking about a few out-of-date courses in some college. We're talking about a major revision in the world of taxonomy where the Linnaean system of taxonomic ranks is what stands accused of being out-of-date. That applies to both your classes and mine.

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After reading Brummitt I should think youd be able to posit your own answer as to why monkeys might be paraphyletic. The answer is because apes are sufficiently modified from Propliopiths (assuming those were our ancestors) to warrant their own family. Since it isnt possible to make all Linnaean taxa monophyletic (without thereby throwing all multicellular life into the species taxon of the first species to evolve), its hardly an exception to acknowledge Propliopiths as being paraphyletic.

And I never said we were talking in this thread about a few out of date courses in some college. You brought up the fact that your college class taught that non-human great apes are pongids. You asked for my reaction, and I gave it your class was out of date on that issue. I havent been able to find anything about the symposium where Brummitt gave his remarks, as quoted in the article, but I find it unlikely that Brummitt would have devoted the vast majority of his time to the question of whether Linnaean ranks can or should be monophyletic, if the actual point of the symposium was to compare the Linnaean system to phylogenetic clades.

Additionally, the primary point Ive asked for your agreement on in this thread is this: Do not imply to people without much biology background that acceptance of evolution requires them to buy into cladistic definitions. (See post 317). Now if hundreds of professional biologists were, as you say, convening a symposium in Washington DC to debate the Linnaean vs cladistic systems, then there must have been at least a few there supporting the Linnaean system. Right? So unless you think those were special creationists, it cant be true that acceptance of evolution requires knowledgeable people to buy into cladistic definitions. Even your own arguments show your position to be untenable.

Cirbryn said:
Families, genera and species, on the other hand, are not used in a purely phylogenetic system.

Aron-Ra said:

But each of the names of those groups may still be applied to comparable clades. There's no reason not to use the same names if they can retain some value that way.

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Those names might be applied to comparable clades, but doing so would affect the status of whatever the group in question evolved from. A clade originates as a branch of a larger clade, of which it is still a part. A Linnaean taxon such as a family, genus or species originates by evolving out of another species, of which it is no longer a part. The existence of the family, genus or species means that whatever it evolved from is paraphyletic. The existence of a clade doesnt mean that.

Also, in many cases there wont be a comparable clade. Linnaean taxa are based on shared characters as well as on phylogeny. Clades are based on phylogeny alone. In Brummitts Figure 1 (2d page) (sorry not to paste it here; the image came out too small), descendants from point 1 have inherited a major character change, while all other taxa have remained essentially unchanged. Clearly the black circles could represent either a family or a clade (discounting what that would do to the taxon from which the black circles evolved), but the remaining white circles can only represent a family, not a clade. They cant be a clade because theyre paraphyletic. We cant break them up into their respective subclades and call each a family, because there are no character differences on which to base the separate families.

Cirbryn said:
As for having to find something halfway between apes and monkeys, however, there assumedly were such species, with some but not all distinguishing ape traits.

Aron-Ra said:

But with all of the monkey traits, just like all the other apes still have. You doubted such a thing existed. I showed you Proconsul, and now you act as if I didn't know about it until you told me. Nice.

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What I said was: Id be interested in any examples you might have of a current scientific consensus that an animal possessing all of the above monkeylike characteristics is an ape. (post 335). The monkeylike characteristics in question were: tails, four-cusped molars, chests that are flatter side to side, etc. Proconsul didnt have a tail. And while there are monkey species living today that dont have tails, those species have four-cusped molars and chests that are flatter side to side.

Aron-Ra said:
But I asked you about finding a species halfway between apes and humans. So I want to know, how does a species halfway between monkeys and apes differ from one halfway between apes and humans? Or one halfway between haplorhines and monkeys? Primates and haplorhines? Archontids and primates?

Sorry, must have misread you. There is no species halfway between apes and humans because humans are apes. There could be species halfway between apes and monkeys (meaning it would have some monkeylike characteristics and some apelike characteristics) because apes arent monkeys. The other groups mentioned fall in the humans-apes type of relationship. (And if anyone is actually trying to look up archontid, as I did, theyll have better luck with archonta).

Aron-Ra said:
You see, proposing a species halfway between apes and monkeys is (to me) no different than proposing one halfway between primates and humans, or halfway between mammals and monkeys.

Yes I know those things are no different to you. Thats because you see everything in cladistic terms. Its not necessary to do that in order to accept evolution.

Aron-Ra said:
I'm still waiting to see any defense that you can make for your single toic exception to these otherwise consistently monophyletic taxons.

The defense (provided above) is that it isnt a single-topic exception.

Cirbryn said:
Those get put into one or the other category with the understanding that they are transitional.

Aron-Ra said:

Thus exhibiting yet another failure of the Linnaean system, one commonly exploited by all of evolution's critics.

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Evolutions critics claim that there arent any transitional species, not that there are many.

Cirbryn · Aug 23, 2006

Response to post 359:

Cirbryn said:
In the same manner we might choose a somewhat arbitrary dividing line to indicate the difference between red and orange on the spectrum. Cladists have similar difficulties identifying where the beginning of a particular clade should be. See the node based, stem based and apomorphy based definitions here.

Aron-Ra said:

The reason this is not so is that the cladistic system doesn't have to wedge anything into one category or the other the way you have to. We don't need a transitional category because, sister groups will continue to grow more distinct, but it isnt remotely possible in any sense to switch from one lineage to another. Cladistics doesn't depend on any paraphyletic dichotomy either, where the moment something becomes a member of the 63rd branch of descent, you have to pretend its no longer part of the 62nd branch anymore. This is because we know that the "distinguishing ape traits" didn't happen all at once, but one at a time, over many many successions. Descent with modification does not and cannot- permit transitional leaps from one imagined category to another.

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I dont know about wedging but cladists do have to decide if a particular species is or is not in a particular clade, and just as with Linnaean taxa the answer is not always easy or obvious. Where on the phylogenetic tree does the clade start? Where, relative to that, is the species in question? Take another look at the three ways to define a clade (see below, from here) and compare it to the following diagram of ape phylogenetics (from Patterson et al 2006. Genetic Evidence for Complex Speciation of Humans and Chimpanzees. Nature 441:1103-08, at 1104. June 29.) Based on the diagrams, as I mentioned in post 380, by a node-based system proconsul would not be an ape; by a stem-based system it probably would; and by an apomorphy-based system it might be, depending on which derived characteristic you chose as determinitive, and on whether proconsul inherited that characteristic from something on the main line to humans or else evolved it independently.

And by the way, Im aware that the Patterson et al diagram supports the idea that apes evolved from monkeys. Given that, and SLPs explanation of his position in post 284, Im changing my position on that point from I dont know to apes evolved from monkeys (barring further information to the contrary). Apes evolving from monkeys always seemed the most likely option, but as I said, I didnt know enough about it to rule out other possibilities such as apes and monkeys evolving separately from tarsiers.

Aron-Ra said:
Phylogenetics is infinitely more realistic, and reflects evolution much better than Linnaean categories for two other reasons too: (1) Everything is a descendant "with modification" just as Darwin suggested. And (2) Linnaen categories commonly generate confusion and impressions of evolution that are actually reversed from the truth. There is the illusion that new species are conceived when two, already different categories interbreed to produce a new lineage between them.

Regarding your first point, this was one of Brummitts primary arguments in favor of the Linnaean system. The modifications are important, and should be reflected by the taxonomic system. Cladistics only groups by descent. It ignores modifications completely.

Regarding your second point, new species are conceived when two, already different categories interbreed to produce a new lineage between them. Its called speciation by hybridization. Its hardly the most common means of speciation, but it does happen. Based on the paper cited above, we humans may constitute such a species ourselves. The fact that cladistics cant handle this kind of speciation, because it violates the assumption of monophyly, is just one more serious mark against using it as a basis of taxonomy.

Aron-Ra said:
This perspective (which is extremely common among creationists) is similar to imagining all your fingers being created out of thin air, and then being blended into one arm; quite the opposite of everything cladistics implies.

I have no idea what this means. Sorry.

Aron-Ra said:
There is also the illusion that at some point, evolution not only permits but actually requires a pronounced macroevolutionary leap from one taxon -recognizeable by a complete collection of characters- into another category which is identified by a different set of characters that aren't shared by its parents. Not only is this never true in any case, (where you say it is true in every case) but it also leads to gradistic thinking; Scala Naturae, from molecules-to-man by way of a stairway of fish to amphibians to reptiles to "mammal-like reptiles" to monkeys to apes to men. With only one notable exception, every twisted parody of evolution that I have ever heard includes one or both of these misconceptions, and Linnaean taxonomy (as you present it) actually promotes both of them!

What do you mean where you say it is true in every case? I never said such a thing. It does occasionally happen, however, that a new species is formed in one or a few generations. Hybridization can do this, as can polyploidy. In monkeyflowers the change from an orange hummingbird-pollinated flower to a pink bumblebee-pollinated flower (and thus from one genetically isolated species to another) can be made with just a few mutations.

As for the perils of gradistic thinking, the phylogenetic tree of life underlying both the Linnaean and cladistic systems does indeed go from molecules (or at least bacteria) to man. It also goes from bacteria to bacteria, and from flatworms (with mouths and guts) to tapeworms (without those things). So the impression of ever-increasing complexity is inherent in the tree; as is its refutation. The Linnaean system merely partitions the tree into categories. It is not responsible for misunderstandings stemming from the tree itself.

The explanation, by the way, for the fact that some lineages have lead to greater complexity while others havent is that evolution causes lineages to become better adapted to their ecological niches, and to attempt to colonize new niches. Often the niches involving less complexity are already occupied, leading perforce to colonization of niches involving greater complexity by those species most pre-adapted to do so.

Aron-Ra said:
Cladistic phylogeny doesn't lead to any of this sort of confusion, nor can it. Go ahead and try to argue how ridiculous it is that you evolved from eukaryotes. Some professional evangelists have tried that with me already and came away with much egg on their faces when I proved that their own mothers and grandmothers were "still" eukaryotes right now.

Yes, and Im sure playing word games like that on professional evangelists gave you a warm fuzzy feeling. But thats all youre doing is playing word games. Our most recent single-celled ancestor was a eukaryote, as are we, but it was also a specific species with many identifying characteristics that we no longer share. All you did was to trick the evangelists into thinking the term eukaryote was one of those identifying characteristics. Cladistics ignores such identifying characteristics completely for species that have given rise to new species, but takes note of them for species that havent. A species once thought to have no descendants has to be cladistically redefined every time a new descendant is found. To coin a phrase, thats just counter-intuitive.

Cirbryn · Sep 15, 2006

SLOWLY I plow! INCH by inch! STEP by step!

(This responds to post 360)

Cirbryn said:
But you may need to be more specific than just "basal therapsids" or "non-avian dinosaurs". Which basal therapsids?

Aron-Ra said:

That depends on whether we're talking about dimetrodon or edaphosaurus, or something else, doesn't it?

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Dimetrodons and edaphosauruses were pelycosaurs, not therapsids. More to the point, one may wish to refer to the entire group of non-mammalian therapsids rather than just one genus or another. With Linnaean taxonomy you can do that. With cladistic taxonomy you cant. Why? Because non-mammalian therapsids and non-avian dinosaurs are paraphyletic groups. They are groups that dont include all the descendants. And it doesnt make them any less paraphyletic to refer to them with unofficial names or to try to identify them by context without actually speaking their names. All that does is point out the inherent awkwardness of the cladistic system.

Cirbryn said:
Where to the "basal therapsids" stop and the "somewhat less basal therapsids" begin?

Aron-Ra said:

Basal therapsids appear to begin before the Triassic and "somewhat less basal" ones come after that. I can refer to the stem groups of a clade without any need of paraphyletic implications.

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I didnt ask where the basal therapsids begin. I asked where they stop. Telling me the somewhat less basal ones come after the basal ones doesnt help much. One of your primary arguments against paraphyletic groups was the difficulty in determining where, on the evolutionary tree, one group ends and a new one begins. The same problem applies to your unofficial groups like basal therapsids, because such groups are paraphyletic. Im not sure what you mean by without any need of paraphyletic implications, but if youre trying to say such groups arent paraphyletic Id suggest looking up one more time what paraphyletic means. A group drawn in such a way as not to include all the descendants of all the members is paraphyletic. The group basal therapsids does not include you and me, but it does include our ancestors. And the fact that cladists are still forced to use paraphyletic groups in their everyday speech, despite working so hard to eliminate paraphyly from their taxonomic system, demonstrates the usefulness and importance of paraphyletic groups.

Cirbryn said:
Presuming the dromaeosaurs were the ones that evolved into birds, you'd be able to talk about tyrannosaurs, because that line died out, but you'd have to call dromaeosaurs "basal birds". Unless, of course, someone happened to demonstrate the exact dromaeosaur species that gave rise to birds, in which case you'd be able to refer to the dromaeosaur species that weren't its direct ancestors as dromaeosaurs, but that one species (and its direct ancestors) you'd have to keep calling basal birds.

Aron-Ra said:

No sir. "Dromeaeosaurs" will do fine, and "maniraptors" is even more precise. "Basal birds" would only be used only if one didn't yet know the specific groups, which I thought we all did by now.

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Alright. I gave that some thought and while youd have to call birds dromaeosaurs, you wouldnt have to call dromaeosaurs basal birds. The bird clade could nest within the dromaeosaur clade but need not extend all the way back to the dromaeosaurs proper. Youd still have to call the dromaeosaurs proper basal dromaeosaurs though, to distinguish them from birds. Cant be saying things like dromaeosaurs are distinguished by a disproportionately large talon on their second toe, since most birds dont have such a talon. (Note: A possible transitional is discussed here)

Cirbryn said:
And how far back along the dromaeosaur ancestral line would you have to go before you wouldn't have a basal bird? All the way to the point just downstream of the bird-crocodile common ancestor? Not much of a bird at that point.

Aron-Ra said:

You couldn't take basal anything- further than the base of that clade. That's kinda what the word means. And at this point, archeaeopteryx is still about as far back as you could take that one. Before that point, you would only be able to list the parent categories that already existed by that time.

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True. And as I discussed above, basal birds was the wrong term anyway. It should have been basal dromaeosaurs. But whereas finding the beginning of basal dromaeosaurs isnt so difficult (once we pick one of the three ways to define a clade, as discussed below), finding where basal dromaeosaurs end is much trickier.

Cirbryn said:
Got any examples of sibling groups in the Linnaean system that aren't related?

Aron-Ra said:

My word, man! Where have you been for the last month? Weren't you paying attention all this time? Siblings are the stem of any two lineages nested within a single shared parent lineage. Linnaean taxonomy actually proposes that two sisters may enter the same family from different parents (polyphyly) or if they have the same parent, they still can't be related to each other because neither of them are related to their most recent common ancestor either. A paraphyletic group means that the descendants aren't part of the parent's biological family anymore, a situation that is impossible in real life. That's why we propose clades.

Click to expand...

Alright, lets take another look at the wikipedia diagram about defining clades:

Sibling groups are so defined because they share a common ancestor. So A and B in the diagrams are siblings that share an unidentified ancestor that lived just before the node where the A and B lines converge. Similarly, Z and (A+B) are sibling groups. So your definition is correct except for its talk about stems.

This brings us to your statement Linnaean taxonomy actually proposes that two sisters may enter the same family from different parents (polyphyly) or if they have the same parent, they still can't be related to each other because neither of them are related to their most recent common ancestor either. I have no idea where you got this, or even what exactly it means. Linnaean taxonomy generally avoids polyphyly, and it does not suggest that a taxon isnt related to its most recent common ancestor.

It also isnt true that A paraphyletic group means that the descendants aren't part of the parent's biological family anymore. A paraphyletic group is simply a group that doesnt include all the descendants. By excluding some descendants, we are not implying those descendants arent related to the parent group. We are implying they have undergone modification to the point that they no longer meet the defining characteristics of the parent group.

Paraphyly wouldnt produce unrelated sibling groups in any case, however. Since sibling groups are defined as sharing a common ancestor, and hence must by definition be related, Im not sure what youre talking about. Possibly you mean to imply that two genera in the same family or two species in the same genus would be siblings of a sort by virtue of sharing the same larger taxon. But since Linnaean taxonomy avoids polyphyly I cant think of any such sibling groups that wouldnt also be related. Thats why I asked you for examples. You havent provided any.

Cirbryn · Sep 15, 2006

(Second part of response to post 360)

Cirbryn said:
Clades aren't objectively verifiable in the sense that we can be sure a given phylogenetic tree is correct.

Aron-Ra said:

Then how could anyone have ever determined that Pongidae needed to be revised? Did they vote on it? If you have a concensus, and some upstart comes along saying he has data which proves everyone is wrong, and which will compell others to change their minds about that even when they don't want to then it is objectively verifiable.

Click to expand...

First off, youre apparently confusing objectively verifiable with objectively falsifiable. Cladograms can be falsified, but they typically cant be demonstrated. They remain hypotheses regarding the true underlying phylogenetic relationships. Thats why papers involving cladograms will typically tell you the methods and assumptions used in generating them, and will also provide the bootstrap values for each node to show the percent of computer-generated trees that show that node using the given assumptions.

Secondly, Pongidae was a Linnaean family, not a clade. I think this is a very important point for getting to the bottom of this argument. On the surface there is no reason why it couldnt be both, assuming it was monophyletic. And if Pongidae were a clade, then leaving humans out of it would indeed be objectively wrong, since clades must include all descendants. The problem with this line of thought only becomes clear when you try to apply it as a general rule. Take another look at the ape phylogeny from Patterson et al 2006 (cited in my previous post).

Suppose we use a stem-based definition of the ape clade (that being the most encompassing), so that it includes the current apes and all their ancestors up to the split from the human-macaque common ancestor. Suppose we likewise define the ape family (Hominidae) to include the same. No problems so far, but now look what that does to groups such as Aegyptipithecus that lived prior to the first ape. Under the Linnaean system, Aegyptopithecus (or whatever was along the direct ancestral line prior to apes) must have had a family too, not to mention a genus and species. So the ape family would have evolved from something in a different family. This means that different family, whatever it was, must have been paraphyletic. So while we can equate the Linnaean ape family with a clade, doing so means that whatever family preceded the apes cant be equated with a clade.

Moreover, the same problem applies within the ape family itself. If we define the orangutan clade (and likewise the orangutan genus) as the lineage from the modern orang back to the common ancestor of living apes, then what genus would we assign to groups such as proconsul that lived prior to the first orang? If you call it some new genus, then that genus would be paraphyletic because it doesnt include orangs. If you call it part of the orang genus, then its still paraphyletic because it wouldnt include the gorilla genus. The same problems apply to the groups on the line between the split-off of the orang and gorilla lines, between the split-off of the gorilla and chimp lines, etc.

So even though clades and Linnaean taxa are both nested hierarchies, they cant be used interchangeably. Linnaean taxa are ranked, and all organisms must belong to a taxon of each rank. Clades arent ranked, but they must be monophyletic. So once we equate a particular clade with a taxon of a particular rank, the requirements of the Linnaean and cladistic systems conflict for the surrounding clades and taxa. By establishing the ape clade as equivalent to the ape family, we make it impossible for the ancestors of apes to be in their own monophyletic family. We also make it impossible for the ancestors of genera within the ape family to be in their own monophyletic genera.

So then how did they determine that Pongidae should be revised? I dont know. The only explanation Ive seen is that humans are more closely related to chimps than orangutans, so it didnt make sense to have a group that included chimps and orangutans but not humans. The problem with that is its just another way of saying the ape family ought to be monophyletic, which as I hope Ive just demonstrated, is possible only at the expense of making everything around it paraphyletic. It shouldnt just be about how closely the groups are related, but rather should include how much the group in question is modified in comparison with the others. Possibly that was considered as well, at least by some, and the answer was that we humans are insufficiently modified from other apes to qualify as a separate family. Im not a taxonomist so I dont really have a good idea about how much modification would typically be necessary. I do note that we are the only habitual biped walkers in the entire synapsid lineage, and our form of bipedalism is completely unique. We differ from bipedal diapsids such as birds and dinosaurs by maintaining a relatively straight line from our shoulders all the way down to our heels. Were also the only primates without an opposable big toe, the only ones with menopause, the only ones with concealed ovulation, and the only ones to occupy boreal habitats. We have the longest childhoods of any primate, and the least sexual dimorphism of any great ape. Theres also all that obvious stuff about brain size, language, tool use, culture, etc. On the other hand most of that stuff has precursers in the other apes: chimps have fairly large brains, rudimentary tool use, culture, communicative abilities, etc. Chimps and orangs can walk bipedally for short distances, etc. So Im not saying it was a clearly stupid decision, I just dont think the one explanation Ive seen is sufficient.

Aron-Ra said:
Wait. Convergent evolution has nothing to do with any of this. It hasn't ever been a part of the topic at-hand and still is not. Let's be clear about that.

Convergent evolution is one of several things that can screw up a cladogram. Relationships are inferred in cladograms based on shared characteristics. Convergent evolution is the means by which two groups might have shared characteristics without being closely related.

Aron-Ra said:
Will you please make up your mind? If phylogenetic trees can ever be shown to be incorrect with additional data, then they are objectively verifiable. If additional data cannot reveal inaccuracies and indicate specific corrections, then it is not objectively verifiable. You can't have it both ways.

No, if phylogenetic trees or cladograms can be shown to be incorrect then they are objectively falsifiable, not objectively verifiable. Wed have to be able to show they are correct for them to be objectively verifiable. We might falsify a particular hypothetical tree, but that tells us very little about which of the many remaining possible trees is actually correct.

Cirbryn · May 26, 2007

Hi folks, Im back. For those who may not remember (or have been trying to forget), this thread turned into a discussion of whether humans are monkeys around post 40 or so and eventually turned pretty acrimonious. Aron Ra dropped out after post 376, and Ive been trying since then to address his remaining posts. Ive taken about a 6 month break, but in honor of Linnaeus 300th birthday (http://www.nytimes.com/2007/05/23/nyregion/23linnaeus.html) Im back at it. (And by the way, it is merely a fortuitous coincidence that my daughter happens to be named Linden). Anyway, this post is in response to post 361.

Cirbryn said:
Since I don't agree that paraphyly is unacceptable, I'm not in a position to speculate as to why it would be. Paraphyly isn't meant to reflect polyphyletic characteristics though. It is meant to reflect the presence of characteristics (either ancestral or derived) that aren't present in the rest of the clade. Cladistics ignores such characters, so cladistics ignores biological information (and in the case of speciation, biological relationships) to make classification easier.

Aron-Ra said:

Whoa whoa whoa! No no no!

Click to expand...

(Sigh).

What, me sigh? Certainly not sir! Clearing my throat was all. No, I just love histrionics! Honest!

Aron-Ra said:
Far from ignoring anything, Ive been demanding from the beginning that you cough up even one generic character common to all monkeys that isnt found in any ape. SLP finally admitted he couldnt do it, but youre still trying to pretend you can. I demand you reveal whatever characters in whatever classes you think Im ignoring.

First of all I said cladistics ignores biological information, not Aron ignores biological information. Not everything is about you personally. I wasnt even talking to you. Secondly, I dont see why you think that making demands about characters that are common to all monkeys but not apes indicates you are far from ignoring anything. I addressed your common characters demand before youd even made it; in my very first post to you (55), where I said: But who says all fish must share the same unique characteristics? . Maybe fish refers to a few specific Linnaean classes. Maybe a fish must have at least four characteristics from a list of six. Maybe the term is somewhat imprecise, as colloquial terms often are, but still clearly leaves out mammals. Ive addressed the topic repeatedly since then as well (e.g. post 292). To review: there dont have to be any characteristics common to all monkeys but not to apes because monkey (like fish) is a colloquial term, not a scientific one. It maps to the scientific terms for several Linnaean families such as Cercopithecidae and Cebidae. Those families have identifying characteristics, but the over-arching colloquial term monkey does not in any official sense. It may be possible to come up with such characteristics, but since it isnt necessary to support the taxonomy, neither I nor SLP have found it worthwhile to try. Also, so far as I can tell after a pretty thorough review of the thread, SLP never admitted he couldnt do it. Your claim to the contrary appears to be just one more instance of you finding something you wanted to see rather than what was actually there. For lots more examples of that: read on!

I did find a very interesting summary of primate evolution here (http://highered.mcgraw-hill.com/sites/dl/free/0072500506/1/26527_ch05.pdf) that does a good job of differentiating apes, and early and late monkeys in an evolutionary context. (Customer Service for the website informs me that the selection is from Cultural Anthropology, 9th ed, 2002, by Dr. Conrad Kottak.) Check out this discussion from page 126:

Some species of Proconsul may have been ancestral to the living African apes. Proconsul also may be ancestral to the Old World monkeys. Proconsul had all the primitive traits shared by apes and Old World monkeys and none of the derived traits of either. Primitive traits are those passed on unchanged from an ancestor, such as the five cusped molars of the apes, which are inherited from an old anthropoid ancestor. Derived traits are those that develop in a particular taxon after they split from their common ancestor with another taxon. Examples are bilophodont molars among Old World monkeys. The Old World monkeys have derived bilophodont molars and primitive quadrupedal bodies. The apes have primitive molars and derived brachiating bodies. Proconsul had both primitive teeth and a primitive quadrupedal body.

Did you catch that? Proconsul (which you called an ape in posts 198, 274, 297 and 343) may have been the ancestor of modern old-world monkeys as well as of modern apes. If true, then by cladistic reasoning old-world monkeys, being descendants of proconsul, would themselves be apes. (Theyd also be Proconsuls, but lets try to not to overly confuse things too early.) Proconsul (the original) might still in turn be a descendant of something youd call a monkey, but all that would do is make modern old-world monkeys both monkeys and apes. Likewise modern apes would be both apes and monkeys. Thats cladistic reasoning for you the distinction of the term ape is completely lost. And the term is in fact distinct, as the paragraph quoted above explains. Apes have primitive 5-cusped lower molars and derived brachiating bodies. Modern old-world monkeys have derived bilophodont molars and primitive quadrapedal bodies. The common ancestor of both had primitive molars and primitive bodies. Since we tend to focus more on bodies, we tend to call those common ancestors monkeys, but we could as easily focus on the dentition instead and call them apes.

I hadnt personally realized until I read the above website that the ape 5-cusped lower molar was the more primitive. Its one of those things that make perfect sense once you think about it. The website (p 126) explains as follows:

As the forests retreated at the end of the Miocene, most apes were restricted to the remaining tropical rain forests in areas of (mainly West) Africa and Southeast Asia. Monkeys survived over a wider area. They did so because they could process leaves effectively. Monkey molars developed lophs: ridges of enamel that run from side to side between the cusps of the teeth. Old World monkeys have two such lophs, so their molars are called bilophodont. Such lophs slice past each other like scissor blades, a good way to shear a leaf.

Moving further out, we get to the new-world monkeys, some of which evolved brachiating bodies independently of the apes. They are distinguished from apes by having an extra premolar, tails, and sideways pointing (platyrrhine) nostrils. These are different distinguishing features than those distinguishing old-world monkeys from apes. Thats why its difficult to find specific characters common to all monkeys but not to apes not because the apes arent distinct, but because they are distinct in different ways from the different families of monkeys. (I discussed this in post 380 as well). As an aside, its suprisingly difficult to find out if New-World monkeys have bilophodont molars. The only example I can find of new-world monkey molars is of the first and second upper molars of the saki monkey (in Mammalogy, 4th ed. 2000. by Vaughan, Ryan and Czaplewski), which appears to show 4 cusps but no lophs. The upper molars of the great apes also have four cusps with no lophs (its the lower molars that have 5 cusps, and only some of those), but the saki cusps appear to have a sharper edge, and they also look more squarely arranged than on ape molars.

As for your demand that I reveal whatever characters in whatever classes I think youre ignoring: again, I wasnt talking about you personally. I was referring to the fact that evolution often produces groups of organisms with characteristics that are noticeably different from their ancestors or from more than one sister group. In order to acknowledge those differences, you need a system that allows paraphyly. For example, in post 354 I posted a cladogram showing 5 major clades of brown bears, and showing polar bears to be a subclade of one of those 5 brown bear clades. Here it is again:

All the clades except that of polar bears share numerous characteristics not shared by polar bears, not the least of which is the capacity to interbreed at significant levels. Thats why brown bears are a separate species from polar bears under the Linnaean system. Yet under the cladistic system there is no way to put all the brown bears into one group and the polar bears into another group. The cladistic rule against paraphyly specifically prevents this. Similarly, as I discussed in posts 318 and 381, if it turns out that one of the species in the Linnaean order Morganucodonta was our ancestor, then Morganucodonta would be an illegal group under the cladistic system, despite the fact that all members of the group share several obvious characteristics not possessed by their putative descendants, such as jaws that hinge at 2 points (4 if you count both sides of the mouth), and articular bones that attach to the dentary. Cladistic taxonomy ignores the unique characteristics of ancestral groups. In fact it ignores the existence of ancestral groups altogether. No cladistically defined group can be ancestral to any other, because if it were that would make it paraphyletic. To my mind, denying the existence of ancestral groups is pretty close to denying evolution itself. Its certainly something the cladists and the creationists can both agree on.

Cirbryn · May 26, 2007

Reply to post 361, part 2.

Aron-Ra said:
I have a laundry list of characters youre ignoring though. Things like what constitutes an stegocephalian, tetrapod, or anthracosaur, and how these are largely retained even by descendant groups (like horses, snakes, and cetaceans) whove reduced or lost only the most obvious of that collection, but retain all the rest identifying their positions still within each of those clades. Linnaean classification ignores biological information, and does so deliberately.

Regarding your laundry list of characters: since this is the first time youve brought it up, I cant reasonably be accused of ignoring it. Also, as I pointed out in post 380, if these are meant to be definitive characters for particular groups of organisms, then every member must exhibit every character. Its not enough to have 9 of 10 or 19 of 20. In either case, the character not universally exhibited by all the members cant be definitive, since it cant be used to define what is in the group and what is not. So when a living or fossil organism is discovered to lack one of the previously definitive characters of its group, then the list of definitive characters must be revised. Thats not actually such a problem for a purely cladistic system such as the PhyloCode, because such a system doesnt have any definitive characters in the first place. Clades are based on descent alone, and any truly cladistic system would reflect that. Characters in such a system are only important insofar as they provide clues regarding patterns of descent. The problem comes when people such as yourself, who apparently dont understand that, go around talking nonsense about how all tetrapods (including snakes) have 4 limbs, to which snakes have added the additional characteristic of having no limbs. (see Post 97). Back in reality, when snakes lost their limbs they no longer met the characteristic of possessing limbs.

Regarding your claim about Linnaean taxonomy ignoring information, lets compare:

Since the Linnaean system allows paraphyly, we cant take two organisms and determine whether one might be a descendant of the other based solely on the Linnaean groups of which they are members. You have to know that from other sources. For instance, Class Reptilia and Class Mammalia have a mother-daughter relationship, while the relationship of Class Aves to Class Mammalia is sister-sister. Thats about it with regard to information ignored or not conveyed by the Linnaean system.

Cladistic taxonomy ignores or misrepresents a whole bunch of stuff. First off, as discussed above, it ignores distinctive ancestral characteristics, and distinctive characteristics possessed by one of multiple sister lines. As a consequence of both these points it cant use the biological species concept (BSC), although many cladists attempt to do so anyway. Thats why the PhyloCode doesnt have species in it. Cladograms are often constructed using species as the basal units, but such cladograms must ignore information indicating that one species is ancestral to another, or that one intra-species clade of several has developed reproductive isolating mechanisms and become a new species. The brown bear cladogram in post 354, for example, identifies the single brown bear clade that became polar bears amid the several other brown bear clades that remain brown bears, but it breaks the rules of cladistic taxonomy to do so. Cladograms are useful taxonomic tools, but the cladistic rule against paraphyly is not.

So there are two ways for cladistic taxonomy to try to handle its inability to use species: either get rid of them entirely, as the PhyloCode attempts to do; or else use them and leave out any information regarding ancestry or the paraphyly of sister clades within the parent species. There are problems with both approaches. If you get rid of species entirely you are forced to work with intra-specific clades, such as the five clades of brown bear from the cladogram in post 354 (reprinted again below). If you do that you give equal status to each of the clades, so the uniqueness of the polar bear is ignored. Furthermore, because all those clades other than that of the polar bear are from the same species, there is nothing inherent preventing them from interbreeding. Cladistics assumes that clades do not interbreed. There is no way to produce monophyletic groups when the history of descent looks like a net (reticulate) rather than like an ever-branching tree.

What would the brown bear cladogram look like if you took the other route and allowed species but ignored information contrary to cladistic requirements? Youd have to treat each species as a separate clade, so all the information regarding 5 separate brown bear clades would be tossed. Then youd have to have the polar bear clade branching off the brown bear clade from a common node. The line leading up to that node would be unnamed. There would be no indication whether that line was itself brown bears (from which polar bears would have evolved), or polar bears (from which brown bears would have evolved), or something else (from which both would have evolved). In fact, if it were any of those three possibilities that would represent paraphyly, so we just have to hope no one asks any embarrassing questions about ancestry at all. Or about whether all the brown bears are actually more closely related to each other than to the polar bears over in the other clade. Because if you can avoid all those questions then it really looks quite tidy.

But wait, theres more! We have not yet plumbed the depths of falseness in this picture. Cladograms, and cladistic taxonomy, assume that a new species is born as soon as it splits from (stops interbreeding with) the parent line. Yet we know this is almost never the case. Generally speaking, a new species is born when a subspecies that has already been isolated for quite some time evolves inherent isolating mechanisms that make future interbreeding unlikely. The following set of diagrams shows the difference between the cladogram and the actual phylogenetic tree: (From M. Sosef, Hierarchical models, reticulate evolution and the inevitability of paraphyletic supraspecific taxa, Taxon 46:75-85, Feb. 1997, at 78).

So then, according to the cladogram we have the following tidy little monophyletic species: a, b, c, d, and e. How many of those are actually monophyletic, as indicated by the tree? The only ones are b and d. All the rest are paraphyletic. The only way cladistics can enforce a rule against paraphyly is to misrepresent the actual evolutionary history of the species being studied.

And were not done yet. Below is another phylogenetic tree from the same source showing some hybrid speciation events (formation of new species due to the interbreeding of members of two other species):

Cladistic taxonomy cant handle this type of situation, with new species seemingly popping up out of nowhere and separate species joining together. Linnaean taxonomy can.

So how often does something like a hybrid speciation event occur? Examples abound, particularly in the plant world. The California wild radish (http://www.sciencedaily.com/releases/2006/07/060713233418.htm), a particular heliconius butterfly (http://www.sciencedaily.com/releases/2006/06/060616135623.htm), and quite likely one of our own recent ancestors (Patterson et al 2006, Genetic evidence for complex speciation of humans and chimpanzees, Nature 441:1103-1108, June 29) were all produced by hybrid speciation. The overall commonness of such speciation is difficult to estimate, but a recent review in Nature (Mallet J, Hybrid Speciation, Nature 446:279-283, March 15) indicates that 40 to 70 percent of plant species are polyploid (meaning they have more than two copies of each chromosome), and probably somewhat more than half of polyploidy events involve the polyploidy of a hybrid (allopolyploidy). Thus perhaps 20 to 35 percent of plant species can trace their evolution back to a hybridization event. And that doesnt even address the hybrid speciations that dont involve polyploidy. Additionally, hybrid speciations may be disproportionately important for evolutionary innovations, because: 1) hybridizations provide additional genetic variation; 2) hybridizations are more likely during times of ecological upheaval when new niches are opening up and adaptive radiations are taking place; 3) the purging of deleterious hybrid allele combinations can change selection pressures on linked genes and allow new alleles a better chance of getting a foothold (Schilthuizen 2004, Hybridization, rare alleles and adaptive radiation, TREE 19:404-5, August); and 4) polyploidy (of which a large proportion is likely to be polyploidy of hybrids) can remove selective constraints on particular genes, allowing one copy to evolve while the other provides the unmodified proteins necessary for survival and reproduction. This last method may explain why fish dominate the worlds oceans today (see Finn and Kristoffersen 2007 http://www.plosone.org/article/fetchArticle.action?articleURI=info:doi/10.1371/journal.pone.0000169).

Any other problems? Cladistics puts closely related organisms into separate groups, and distantly related organisms into the same group, despite the fact that it was specifically intended to avoid that. For instance, cladistic analysis groups humans with other apes on the basis of our very close relatedness to chimps. Yet it also puts the first member of the human line (after the split from the common ancestor) in a separate group from the first member of the chimp line, despite the fact that those two species would have been more closely related to each other than either is to humans or to chimps. To quote Richard Brummitt (quoting in his turn Ernst Mayr) (http://depts.washington.edu/phylo/LabMeetingReadings/Week1/BrummittParaphyly2.pdf p 38): According to cladistic principles, the modern descendants of Charlemagne are more closely related to him than he was to his brothers and sisters.

And were not done yet. The single most important advantage cladistic taxonomy is supposed to have over Linnaean is its reproduceability. Different taxonomists with the same data are supposed to come up with the same group divisions using cladistics, whereas using Linnaean taxonomy there is supposedly too much room for personal bias. Yet a close examination of cladistic methods shows this reproduceability to be illusory. As Cela-Conde and Ayala note (in Genera of the Human Lineage. PNAS. June 24, 2003. http://www.pnas.org/cgi/reprint/100/13/7684): This [cladistic] procedure, of course, assumes that all of the taxa examined are the results of lineage splitting and do not represent stages in a lineage. Claims of objectivity notwithstanding, the matter of which cladogram is best depends largely on the decisions made at each step. But no step is free from difficulties. For example, does the fragmentary cranial vault and face KNM-ER 2602 of Koobi Fora (Kenya) pertain to the hypodigm of A. afarensis or to that of Australopithecus boisei? Do Homo habilis and Homo rudolfensis represent one or two species? Does H. habilis exist at Sterkfontein (South Africa) or must the Stw 53 and Sts 19 specimens be regarded as A. africanus? The way in which the species are chosen and the hypodigms are constructed leads to very different cladograms.

Theres also the nomenclatural limbo I mentioned in post 381. Often you dont know if a given group gave rise to descendant groups or not. You may find some evidence indicating they did, and then later find more implying they didnt. If they didnt, then the given group would be valid by cladistic standards. If they did, then it wouldnt. So you can have a group that shifts wildly in its listed characteristics in an effort to include or exclude other groups that may or may not have descended from it. For instance, if the morganucodonts turn out to have been our ancestors, then cladistically wed all be morganucodonts, so we couldnt describe them as having two jaw hinges and fused articular and dentary bones. If they turn out to have died out without descendants, then we can describe them that way. If conflicting evidence keeps coming in, then theyll flop back and forth possibly for years.

(Continued next post)

Cirbryn · May 26, 2007

Response to Post 361, part 3.

Finally theres the problem caused by people such as yourself who think all Linnaean taxa can be made into clades. It should be blindingly obvious that this is impossible, since paraphyly is integral to the Linnaean system. As I pointed out in post 383: A clade originates as a branch of a larger clade, of which it is still a part. A Linnaean taxon such as a family, genus or species originates by evolving out of another species, of which it is no longer a part. The existence of the family, genus or species means that whatever it evolved from is paraphyletic [and thus not a clade].

Now often so little information is available that many of these problems can be downplayed. For instance, the problem of cladistics failure to account for distinctive ancestral characteristics isnt so much of a problem if you dont have any potentially ancestral fossils to worry about. As it happens, there is now a good fossil record for the human line subsequent to the split from the chimp common ancestor, so we should all take a moment to pity the poor sods attempting to apply cladistic reasoning in this area. A good example is The Human Genus, by Wood and Collard, Science 284:65 (1999), in which the authors examine the genus Homo to see if it is a good genus by cladistic standards. The authors analyze various cladograms comparing several fossil hominins and conclude that Homo habilis and Homo rudolfensis are more closely related to the Australopithecines than they are to H sapiens, and that therefore habilis and rudolfensis should be transferred to the Australopith genus. Does this straighten things out? It does not. They state: The transfer will almost certainly make Australopithecus paraphyletic, and the genus will subsume an impressive range of cranial morphology (9, 44), but we favor this option because it is taxonomically conservative. So they solve the problem of paraphyly in the genus Homo, only to increase the paraphyly of the genus Australopithecus (which of course would already have been paraphyletic due to the fact that the genus Homo evolved from it). Furthermore the supposed paraphyly they found in Homo wasnt really there in the first place. H habilis and H rudolfensis are very early Homo species. Of course they are going to more closely resemble some of the Australopiths (from which they had only recently split) than they are Homo sapiens, which evolved some 2 million years later.

Aron-Ra said:
In fact, at the PhyloCode symposium, Richard Brummitt actually shouldnt reflect evolutionary relationships at all. Instead, he said we needed two systems; he promoted his beloved Linnaean system for classification, but he insisted that it is incompatible with the evolutionary phylogenetic scheme, and shouldnt be used to indicate evolutionary relationships.

All of which would be much more convincing if it wasnt completely wrong. (1) There was no Phylocode symposium; (2) Brummitt never claimed taxonomy shouldnt reflect evolutionary relationships; (3) nor did he claim that we need two systems; (4) nor that the Linnaean system is incompatible with the evolutionary phylogenetic scheme; (5) nor that the Linnaean system shouldnt be used to indicate evolutionary relationships.

(1) The symposium to which youre assumedly referring (in which Brummitt gave this presentation http://depts.washington.edu/phylo/LabMeetingReadings/Week1/BrummittParaphyly2.pdf) was called Linnaean Taxonomy in the 21st Century (see p 3 of http://www.nmnh.si.edu/botany/plantpress/vol4no2.pdf). It was conducted in March 2001, was attended by plant taxonomists, and was specifically intended to focus on the Linnaean system, not on the PhyloCode. Five papers resulting from the symposium (including Brummitts) were published in volume 51, No 1 of the journal Taxon (published by the International Association for Plant Taxonomy).

(2) Brummitts actual claim here was that taxonomy cant (and shouldnt try to) reflect *all* evolutionary relationships, not that it shouldnt reflect any. He acknowledges that Linnaean taxonomy doesnt reflect all relationships, and points to where cladistic taxonomy fails to do so as well (for instance at p 38). The main point of Brummitts article isnt to attack purely cladistic systems like the Phylocode, however, (which he says isnt likely to be generally adopted anyway). Rather, it is to attack the practice of applying the cladistic requirement of monophyly to Linnaean taxa. The Linnaean system, he argues, is inherently incompatible with a monophyly requirement, and this is a good thing because paraphyly allows Linnaean taxa to reflect both descent and modification.

(3) Brummitt never said we need two systems. His point was that the job of taxonomy is to make useful and meaningful categories out of the underlying tree of life to chop up the tree. Thus he was talking about the taxonomic system and the underlying tree as being two separate and necessary things. He was not talking about any need for two taxonomic systems.

(4) Brummitt never argued that the Linnaean system was incompatible with the evolutionary phylogenetic scheme. He argued that they werent the same thing. The evolutionary phylogenetic scheme is the underlying tree of life. Linnaean taxonomy (and all taxonomies) divide that underlying tree up into categories. Brummitt did argue that Linnaean taxonomy is incompatible with a requirement of monophyly, but thats not the same thing. I explained all this at the end of post 382 as well.

(5) Brummitt never said Linnaean taxonomy shouldnt be used to indicate evolutionary relationships. He merely acknowledged that it doesnt indicate *all* such relationships because it instead provides information about evolutionary modifications (character differences) along a given branch of the the underlying tree.

Cirbryn said:
Assuming apes evolved from monkeys,

Aron-Ra said:

Thats funny. You say that as if there was still some other option, as if you didnt already know that every single proposed ancestor of Hominoids wasnt described as a monkey by scientists in this field.

Click to expand...

See the discussion about Proconsul, post 387 above.

Cirbryn said:
the apes did indeed become so derived that they formed another group (which is monophyletic), thereby making monkeys paraphyletic.

Aron Ra said:

No sir. That would be no different than claiming mammal was paraphyletic just because were so derived. It doesnt make any sense and theres no justification for it in either case. Monkeys (anthropoidea) is no less monophyletic than Theria.

Click to expand...

Im really tired of this complaint (I wont even call it an argument). If it doesnt make sense to you thats fine, but that doesnt mean it isnt true. Evolution doesnt make sense to the Creationists either. Thats because, like you, they cling to incompatible assumptions that they are simply unwilling to seriously question, even to the extent of acknowledging the existence of alternative possibilities. The Creationists underlying assumption is that the characteristics of individuals in a species tend to vary around some kind of unchanging archetype, rather than around the characteristics of their parents. Your assumption is that we cant divide the branches of the tree of life to indicate different groups. Im here to tell you we can make groups that way, and we do. Brown bears evolved into polar bears, after which they were no longer brown bears. Something that looked somewhat like modern monkeys, but with apelike teeth, left some descendants that evolved into modern old-world monkeys and some that evolved into apes. Things evolve into other things. You and the creationists may not like having your assumptions called into question by that fact, but that doesnt make it untrue.

And monkeys is not the same as anthropoidea.

Cirbryn said:
I'm not aware offhand of any common characteristics of greater monkeys (by which I assume you mean Simiiformes) that evolved independently, except possibly for tricolor vision. I don't agree that means they are better classified as a monophyletic group, and even if I did agree it wouldn't matter, since they are not so classified.

Aron Ra said:

Yes they are. Have we not clarified this enough by now? The Simiiformes taxon is the exact same thing as the anthropoid clade. Both of them monophyletic.

Click to expand...

Well the anthropoid clade includes tarsiers, while the Simiiformes infraorder does not, so theyre not the same thing. But you are right that Simiiformes is monophyletic. What youre wrong about is your assumption that monkey means either anthropoid or simiiform. Monkey means a member of any of the following families: cercopithecidae, cebidae, aotidae, pitheciidae or atelidae. The term may also be applied to some of the families that were directly ancestral to those, but its a judgement call as to how far back you can go (if at all). It does not apply to the families hylobatidae or hominidae (the latter being the family to which humans belong). The fact that it isnt clear exactly which ancestor, if any, should be called a monkey means the term monkey is not well defined. Many words in the English language that arent used in formal classification schemes are similarly indistinct. Deal with it.

Cirbryn said:
You hadnt explained that you always make clear to others that you are speaking non-paraphyletically.

Aron Ra said:

Yes I did -frequently.

Click to expand...

Aron Ra said:

Cirbryn said:

Such as?

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Cirbryn said:

Aron Ra said:

What do you mean, "such as"? This question doesn't make any sense. Don't you bother to even read what you're replying to?

Oh yeah, I forgot. You already told me you don't. So I suppose I should answer this comment the way I've answser most of your comments in this thread: Go back and read the whole post this time.

You want me to show you again what Ive already shown you before.
Why should I show you again, what I know youll only ignore?

Click to expand...

Click to expand...

Click to expand...

See this is the kind of thing that Id normally just skip over. Its just snitty. Nevertheless, since Im trying to plow through everything:

By such as I meant such as where. Meaning please provide a citation. I think that should have been fairly obvious.

I dont think I ever told you I dont read what Im replying to. The closest I came was mentioning in post 204 that I was scanning through the off-topic points in your post so as to reply to the parts that were relevant to the question of whether humans are monkeys.

I also dont think you provided any examples of the requested cites previously. I think this is just another case of you misreading or misremembering whats actually been said. Further examples of that are provided at the beginning of this reponse to post 361, and in posts 368 and 380 (not to mention your summaries of Brummitts paper above and farther down).

Nitron · May 26, 2007

Threadomancy?

Cirbryn · May 26, 2007

Response to Post 361, Part 4:

Cirbryn said:
Im concerned that you are damaging the general acceptance of evolution by suggesting there is a scientific consensus that humans are monkeys, when in fact there isnt.

Aron Ra said:

I have never made that argument. I've never argued for a consensus of any kind.

Cirbryn said:

Then why did you claim in post 327 that paraphyly is not acceptible in taxonomy anymore? Are you trying to claim its unacceptable even though many or most taxonomists accept it?

Aron Ra said:

No, Im claiming its unacceptible because many or most taxonomists say its unacceptible. Honestly, if I hadnt happened across those comments from Richard Brummitt, I wouldnt have guessed that there were still people like you out there. And you're fortunate that I found his treatise, alleging all the absurd things that he does, otherwise I would have accused you of trolling, and of being intentionally absurd. I don't know. Maybe that's what he was doing too. But even in Brummitt's address to the PhyloCode symposium, he pleaded for his fellow taxonomists to reverse their current stance by making paraphyletic taxa acceptible, where at present, he said, they are not acceptible, and particularly not in such strict scientific literature as a doctoral thesis. Youll love his reasoning too. He wants paraphyletic groups because people like them, its tradition, and old habits die hard. Real scientific there. He also described paraphyletic taxa as evolutionary leftovers. If that aint gradistic thinking, what is?

Click to expand...

Click to expand...

Click to expand...

First you say you youve never argued for a consensus of any kind, and in the next breath you say paraphyly is unacceptable because many or most taxonomists say its unacceptable? If that isnt an argument based on a perceived concensus, then what is it? Regardless Ill rephrase the original statement: Im concerned that you are damaging the general acceptance of evolution by suggesting that, scientifically speaking, we are monkeys. In fact we are only monkeys cladistically speaking, and even thats debatable.

I will admit to being surprised at Brummitts suggestion that numerous taxonomomists apparently think the Linnaean system can be made to exclude paraphyletic taxa. That is objectively incorrect, not just a matter of preferring one taxonomic system over another. (I discuss why in post 386. Brummitt explains it as well in his How to chop up a tree paper). My impression is that thanks to the efforts of people like Brummitt and Sosef (on the Linnaean side), and DeQueiroz & Gauthier (on the cladist side) (see e.g. p 32 of Brummitts paper), most taxonomists are coming to realize this. Also supporting this trend is the Wiki article on Synapsida (http://en.wikipedia.org/wiki/Synapsida) which states: The traditional classification continued through to the late 1980s (see e.g. Carroll 1988). In the 1990s this approach was replaced by a cladistic one . A recent, compromising position (see Benton 2004) has the class Synapsida as intentionally paraphyletic. I think many of the taxonomists who were previously pushing for eliminating paraphyletic Linnaean taxa are now pushing the idea of a rank free classification scheme that essentially amounts to using cladistic taxonomy down to the species level, but keeping the Linnaean rank of species. I call this progress, since they have apparently realized the Linnaean system in general cant be made to follow cladistic rules. I expect in another 5 or 10 years theyll also come to realize that species cant be made to follow cladistic rules either. At that point theyll have to either switch to the PhyloCode or to Linnaean taxonomy, and well be done with these silly attempts to make Linnaean taxa monophyletic.

As for your further attempts to summarize Brummitts address to the 2001 Linnaean Taxonomy symposium (not the PhyloCode Symposium), you are so impressively wrong as to lead me to conclude that you are simply making these phrases up and attributing them to him. I ran a word-search of his paper for the direct quotes you provided. Heres what I found: people like them 0 matches; its tradition 0 matches; evolutionary leftovers 0 matches; old habits die hard 1 match.

Heres the context of that one match:

Four years ago I felt confident enough of my arguments to challenge one of my opponents to a debate at the Linnean Society of London. The motion was thought up by a colleague, not me, and was That this House considers that Linnaean classification without paraphyletic taxa is nonsensical. To the surprise of many people, this motion was passed by a vote of 69 in favour to 43 against. When the vote was announced, three people present separately said to me that the only surprising thing was that 43 people could vote against the motion. But old habits die hard, and one still sees statements in taxonomic papers that genus A nests within genus B and therefore has to be sunk irrespective of the characters by which it is distinguished. This is why I said I thought that our taxonomy was going off the rails. However, I think the pendulum is swinging away from what I call the old-fashioned Hennigian view of taxonomy into a more modern and realistic view appropriate for the 21st century. (http://depts.washington.edu/phylo/LabMeetingReadings/Week1/BrummittParaphyly2.pdf pp 40, 41)

Aron Ra said:
The only reason the Buddhists were frustrated with me was they had no choice but to accept those definitions. What choice did they have?

I seriously doubt that was the only reason they were frustrated with you. But getting back to the point you were attempting to make with that digression into Buddhism in post 339, you claimed that the idea that humans are monkeys is objectively demonstrable that the idea is independant of the vagaries of the particular taxonomic system chosen. As far as I can tell youve never expanded on that claim and actually attempted to demonstrate this objective proof. All your arguments have been based on the idea that humans are monkeys because they are descended from monkeys. Yet it is not objectively demonstrable that an organism must be considered a member of the group from which it is descended. The Linnaean system specifically rejects that precept. Ergo your arguments are not reality-based, they are based on the acceptance of your particular taxonomic system and its underlying assumptions.

Aron Ra said:
Robert DeFilipps of the Smithsonian Museum wrote that this symposium was meant to determine whether the Linnaean system still works, and what had to be done salvage it. The consensus he reported was that the Linnaean system required a serious overhaul that takes into consideration modern concepts of evolution and phylogeny" which it currently does not, and if Brummitt has his way, it never will.

First off, if youre going to quote someone, you need to provide the cite. I googled Robert DeFillips and serious overhaul and found a single match (http://www.nmnh.si.edu/botany/plantpress/vol4no2.pdf, p 3). Based on that document, the author of your quote was W. John Kress, not Robert DeFillips. The quote, in context, is as follows: The consensus that emerged was that the solution does not reside in a replacement of the current Codes, but in a serious overhaul that takes into consideration modern concepts of evolution and phylogeny. Linnaeus will survive this challenge and will be better for it in the 22nd century. Given the last sentence, it isnt clear to me what Kress had in mind by serious overhaul, but I dont think it means replacing it with a cladistic system. Frankly I dont find one persons attempt at summarizing the views of various plant taxonomists at a single symposium in 2001 to be particularly telling anyway. For what its worth, the abstracts of the speakers at the symposium are provided on page 8. Based on those, Id summarize each speakers presentation as follows:

Nicolson: General history of Linnaean system.
Brummitt: Linnaean system is preferable and must include paraphyly.
Berry: Linnaean system has a few problems but generally works fine.
Mishler: Dump ranks including species use clades.
Forey: PhyloCode has problems.
Stevens: Philosophy of taxonomic nomenclature in general.
Wilson: This isnt a good time to change things.

Of those, only Mishler favored replacing the Linnaean system with something cladistic.

Aron Ra said:
Mine is the opinion of most taxonomists. But as I said, it doesnt matter what anyones opinion is; there is objective criteria to examine here, criteria you persistently dismiss always pleading for an argument from authority instead.

I dont think yours is the opinion of most taxonomists, and I think it is becoming less and less common as time goes by. I also think that your opinion is much more rare among biologists in general, including evolutionary biologists. I also dont think there are any objective criteria that would allow us to conclude that humans are monkeys. Your conclusion to that effect is based on an a-priori assumption that an organism must belong to the same taxonomic group as its ancestors. There are no objective criteria to support that assumption, and the assumption is not compatible with the Linnaean system.

As for my argument from authority, I see a difference between how things are organized and how they perhaps ought to be organized. Under the current system, which is the Linnaean, apes and monkeys comprise separate groups of families. Thats just the way it is. If you come upon table settings in which the forks are all to the left of the plates, it doesnt help you to pretend theyre really all to the right. They remain to the left because whoever set the table organized them that way. If you think they ought to be organized differently you are welcome to say so, but even if you were convincing in your arguments that wouldnt change the actual position of the forks until someone switched them around. Ive never said the Linnaean system ought to be used because the authorities say so. Ive said: 1) it is being used; and 2) it ought to be used because its a better system.

Cirbryn · May 26, 2007

Nitron said:
Threadomancy?

Actually, rumors of thread death have been slightly exaggerated.

Lilandra · May 26, 2007

Aron is currently banished for a period from the forum for saying Creationism relies on falsehoods,

Although your in depth replies are refreshing compared to creationist illogical replies.

Punchy · May 26, 2007

MewtwoX said:
I think a picture will make it clear:

The general nature of the fossil record, of the abrupt appearance of types with variation within types, is more like a lawn than a tree.

Brennin · May 27, 2007

Army of Juan said:
Humans are apes, our ancestors were ape-like. Why is that so hard to understand?

Pull the other leg.

Galle · May 27, 2007

Lilandra said:
Aron is currently banished for a period from the forum for saying Creationism relies on falsehoods,

It says something highly unflattering about Christian Forums that it should ban a highly intelligent and polite man for telling the truth while allowing dishonest curs to spread their libel.

Dannager · May 27, 2007

Punchy said:
The general nature of the fossil record, of the abrupt appearance of types with variation within types, is more like a lawn than a tree.

No, not really. In fact, not at all.

Galle · May 27, 2007

Punchy said:
The general nature of the fossil record, of the abrupt appearance of types with variation within types, is more like a lawn than a tree.

I await, with great anticipation, your support for this statement.

I must admit, I am mystified as to why you didn't support it in the same post in which you made it.

Dannager · May 27, 2007

Galle said:
I await, with great anticipation, your support for this statement.

I must admit, I am mystified as to why you didn't support it in the same post in which you made it.

Perhaps because no credible support exists? It's easy to make ridiculous claims when you don't have to back them up.

Cirbryn · May 27, 2007

Lilandra said:
Aron is currently banished for a period from the forum for saying Creationism relies on falsehoods,

Wow. I wonder what CF rule they're claiming that violates. I also wonder if they realize how poorly actions like that reflect on Christianity in general.

I never actually expected Aron to reply however (although he's welcome to, of course). He did say he was done. I'm just trying to get through his final posts - mostly for my own benefit (I've learned a lot by looking into all this stuff) but also because if the topic comes up again in another thread I'd like to be able to refer people here.

Lilandra said:
Although your in depth replies are refreshing compared to creationist illogical replies.

Well thanks. And as an X-Men fan allow me to offer my compliments on your new name.

Did you say Evolution doesn't teach man evolved from ape?

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