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

[Aron-Ra]

If they asked me about the difference between apes and hominids, and my grade wasn’t affected by my answer, I’d probably mention that great apes and hominids (family Hominidae) are the same thing under the currently accepted system, but that the difference between the subtribe Hominina (which previously was termed “hominids”) and other apes includes upright stance and an unapposable big toe.

My position is that “apes” includes Hominidae (which includes the species previously assigned to Pongidae) and Hylobatidae. I presume the last common ancestor of Hominidae and Hylobatidae would be considered an ape, but I don’t really know for sure.

How would you determine that?

Polyphyly is avoided in the Linnaean system,

Were that so, then you shouldn't have said that all monkeys were either in the Old World or New World sister taxons.

but the term “ape” isn’t Linnaean. It’s just associated with two separate Linnaean families. Accordingly the term “ape” might possibly be polyphyletic.

The word, "ape" is associated with Hominoidea, that's one monophyletic taxon, not two.

Claiming that New World monkeys and Old World monkeys each became monkeys separately because their common ancestor was not a monkey – is exactly no different than claiming lesser apes and great apes each became apes separately, because their common ancestor was not an ape. How is any of this paraphyly or polyphyly justifiable in your perspective?

I agree the situations would be equivalent. As with my answer to apes, I don’t know that old and new world monkeys evolved separately from a non-monkey. I’m just saying that as far as I know it’s a possibility. I “justify” the resulting possibility of polyphyly in the term “monkey” or “ape” by noting that those aren’t Linnaean terms. I don’t consider the English language in general to have any restrictions on polyphyly.

All the potential grandfathers of Catarrhini were described as monkeys, and all the potential grandfathers of both Old and New World monkeys was also described as "monkeys" by your own cited authorities in both cases; and they were all collectively categorized as 'simians' which means the same thing.

If a species that looked human evolved from existing chimpanzees, I expect it would be given separate genus and species names rather than being placed within Homo sapiens. To place it within Homo sapiens would imply we could interbreed with them, which would be extremely unlikely. They might still be referred to as “humans” though. There aren’t any nomenclature cops for non-Linnaean categorizations.

You're not talking about non-Linnaean categorizations. One can be Homo -without being sapiens- and still be human. You can have multiple species of humans under either system. But the point of course is that you can't have multiple sorts of any classification if they did not emerge from the same ancestral source.

If you’d like I can provide a short “defense”, but I’m not going to go off on a tangent regarding it because it’s not germane to the question of what the scientific consensus actually is. A descendant group can evolve out of the parent category by losing the defining characteristics of that category.

Name one example where that has ever happened; where the new emergence was no longer defined by the total tally of all the parent clades collectively, -in addition to the new alteration.

By recognizing that a newly evolved species is no longer part of the old species, we acknowledge it has lost the defining characteristic of the old species – that being open gene flow. There is no denial of phylogeny in such a practice – nothing to say species B didn’t evolve from species A – just a lack of information one way or the other within the taxonomic system. By demanding a “separate box for every new species” we identify groups that are separated by gene flow from all other groups. This is phylogenetically important because it means those groups are evolving separately from all other groups.

In that case, how would you treat this hypothetical situation:

Imagine the "ostrich" tribe isolated themselves culturally, and developed some genetic barrier to reproduction with other humans. We would doubtless call their clade, Vadoma, as we do already. But would we no longer consider them Homo sapiens anymore?

Regarding “uneven ranks”; there is admittedly a lot of subjectivity regarding (for instance) what constitutes a class versus an order versus a family in different lineages. I don’t see that as a major problem, however, since they constrain each other within each lineage such that the class must be more inclusive than the order, which must be more inclusive than the family.

Truthfully, the only issue I have with them is when we start to apply rules to classes we made up and which nature doesn't have to aknowledge. How can we really tell whether we're looking at a different genus as opposed to a subgenus?

 

[Lilandra]

"Even if something is misclassified" according to what classification system? If it were misclassified according to the system it supposedly represents, that would be one thing, but Aron isn't claiming that by the Linnaean system humans should be monkeys. He's claiming humans are monkeys according to an entirely different system. Fine, then who uses that system?

Within thought systems, there are paradigm shifts. An analogous school of thought would be Newton's work on gravity and Einstein's Theory of Relativity. Newton's work is still useable but Einstein's work is more elegant.

Cladistics is a refinement of traditional taxonomy. It is more organic and thus reflects a biological system better. As to who uses it, it is better to be ahead of the curve of a paradigm shift than behind it.

]Is it generally accepted in the scientific community or not? Aron is implying to people that if they don't accept this alterative system they'll be unscientific. Is that true or not? To answer those questions you have to look at which system is generally used in the scientific community.

I am not sure that he is implying that. But it would seem that science is about following evidence where it leads not guarding old paradigms.

 

[Aron-Ra]

Additionally, the species rank is not uneven, since all species have the same defining characteristic. This helps provide a sort of ground floor against which the differences of genus, family, etc, can be measured in each lineage. Balancing the drawbacks to the subjectivity of ranks above the species level, we get the advantage of being able to give a particular name to the progenators of a particular clade that all share certain characteristics (rather than having to refer to them as the proginators of a particular clade that all share certain characteristics). Under the Linnaean system we can refer to the morganucodontids, for instance, or the cynodonts, or the pelycosaurs.

As I already explained, you can do that with the phylogenetic system too, and still be easily understood when the context includes all the descendants as well.

The pelycosaurs may have been a worse example than I’d intended, however, since apparently they now include pretty much everything in the synapsid clade other than the therapsid clade. (Several sites talked about similar skull characteristics among the pelycosaurs, but I couldn’t tell to what exent the early Therapsids shared those characteristics). On the other hand, maybe it was an unconsciously good example, since (assuming apes and present-day monkeys all form a single clade),

They do; Anthropoidea.

this would put the pelycosaurs in a similar position to the monkeys. Pelycosaurs would be non-therapsid synapsids, just like monkeys would be non-hominoid anthropoids. Even from a cladistic point of view that should be pretty straightforward. Just start with the larger clade and subtract out the smaller one.

I also found some discussion directly on the topic of how the consensus has been shifting around regarding the synapsids. The synapsids are a confusing group, because the name could refer either to the synapsid clade (of which we are members) or to the paraphyletic Linnaean order Synapsida (of which we aren’t). The above link to the wiki article has the following to say:

“The traditional classification continued through to the late 1980scladistic one, according to which the only valid groups are those that include common ancestors and all their descendants. Because Synapsids evolved into mammals, the mammals therefore are included under the Clade Synapsida. (see e.g. Carroll 1988). In the 1990s this approached was replaced by a

A recent, compromise position (see Benton 2004) has the class Synapsida as intentionally paraphyletic, constituting a grade of animals from the earliest split with sauropsids to the arbitrary division with its daughter class, Mammalia.”

So you’re correct that there has been significant movement away from the Linnaean system in certain areas.

Primarily paleontology, my field of interest.

I don’t consider that to indicate a general shift to a purely cladistic system, because such a system would include a cladistic definition of species, and although such a definition does exist, it doesn’t seem to have claimed many adherants (with possibly the most notable and passionate exception being Joel Cracraft).

Some years ago, when I put up a site about the evolution of ratites, I read a lot of Cracraft's work. But I don't think I saw what you saw. Do you have a citation?

I expect that’s the main reason why the PhyloCode doesn’t seem to be going anywhere.

I wasn't aware of that either.

But if revisionists don’t put forth an alternative system, but instead just redefine an existing Linnaean group to be monophyletic, how does that constitute a movement away from Linnaean taxonomy?

Call it a tendancy to lump rather than split. If we concentrate on differences, we can isolate any one man apart from all other men. Citing such differences leads to prejudice. So we observe similarities instead, with quite the opposite result.

The only way it would is if they advocate calling it a clade without assigning it a Linnaean rank. That’s what the above quote indicates was done during the ‘90s with class Synapsida. Even then, the quote indicates they were avoiding confusion by calling it Clade Synapsida. Now with Benton the momentum seems to be shifting back towards class Synapsida. Under such circumstances, you have to identify whether you’re talking about the class or the clade.

Understand that the names of the ranks often have some value, especially when educating others on what taxonomy is all about. But the rank itself, the fact that it is a rank- is the problem. Because in reality, they're not ranks; they're certainly not equal. They're just points at which sister branches emerged from the same limb.

As far as I know, there has not been a similarly well-embraced movement towards doing away entirely with the Linnaean ranks applicable to monkeys and apes. The great apes were placed in family Hominidae, not taken out of all Linnaean families and referred to simply as the ape clade.

But that's exactly what Hominoidea is.

Accordingly, that change is within the Linnaean system. With the exception of moving the tamarins and marmosets from family Callitrichidae to family Cebidae (which I’m not sure has been generally accepted - for instance see here) there doesn’t seem to be much call for shaking up the monkey classifications. Accordingly, it looks clear to me that the consensus taxonomy for monkeys and apes is Linnaean. And I’ve seen nothing from you to contest that.

Yes you have -in post #201.

“Linnaean definitions have important nomenclatural consequences. Because Linnaean definitions are based on the Linnaean categories, categorical assignment plays an important role in the application of taxon names. …For the modern biologist, however, association with one of the Linnaean taxonomic categories is not the most relevant aspect of meaning. As a result of the intellectual revolution brought about by the acceptance of an evolutionary world view, taxon names now have at least implicit evolutionary meanings. In other words, a taxon name has an association not only with one of the Linnaean categories, but also with a particular part of the evolutionary history of life. …For anyone who thinks that taxonomy ought to represent something about evolutionary history, this second aspect of meaning is not trivial. This situation explains why biologists often express annoyance about proposals that would change the implicit phylogenetic meanings of taxon names.”
--Kevin de Queiroz; Consequences of (Problems with) Linnaean Definitions, Biological Nomenclature in the 21st Century

Additionally, you would only be justified in implying that paraphyletic groups are unacceptable among biologists if the consensus had swung completely over to the cladistic side. If the consensus were up in the air (much less on the Linnaean side), then it would be a lie to tell people the “scientific viewpoint” is to avoid paraphyly.

Not when they can see that reflected in definitions written by scientists.

"Over time, our understanding of the relationships between living things has changed. The greatest change was the widespread acceptance of evolution as the mechanism of biological diversity and species formation. After this, it became generally understood that classifications ought to reflect the phylogeny of organisms, where each taxon should originate from a single ancestral form. Such taxa are designated as being monophyletic. In modern systems it is generally encouraged that taxa should be strictly monophyletic."
--Wikipedia

"The general approach Linnaeus took to classifying species and many of his taxonomic groups have remained standard in biology for at least two centuries. It is now generally accepted that classification should reflect the Darwinian principle of common descent, so that taxa include a single section of the evolutionary tree. Such groups are called monophyletic groups."
--Biocrawler: "scientific classification"

Of course there are many other sources for this, enough for anyone to see that I'm not lying about the scientific position.

Similarly, monkeylike characteristics (such as tails, four-cusped molars, chests that are flatter side to side, etc.) were present in several families of species living about 30 or 40 million years ago, one of which may have been our direct ancestor.

And all of which were described as monkeys, apes, monkey-like apes, ape-like monkeys, and/or “ape-like hominids”, both by the common laity, and by scientists in that field.

I’d 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.

OK, but you're asking for something I've already shown you again. I have to repeat myself an awful lot in this thread!

Not all the characteristics above are applicable. As I told you before, Aegyptopithecus, (and Victoriapithecus too I think) had five cusped molars while most callithricines have only three. So the number of cusps aren't descriptive of all monkeys, and Aegyptopithecus is considered a monkey.

"Monkeys evolved from prosimians during the Oligocene or slightly earlier. They were the first species of our suborder--the Anthropoidea. Several genera of these early monkeys have been identified--Apidium and Aegyptopithecus are the most well known."
--Palomar college, San Diego

Proconsul is considered an ape, but with the characteristics consistent with the traditional classification of monkeys.

"Among the oldest known hominoids is a group of apes known by its genus name, Proconsul. Species of Proconsul had features that suggest a close link to the common ancestor of apes and humans. The ape species Proconsul heseloni lived in dense forests of eastern Africa about 20 million years ago. It was agile in the trees, with a flexible backbone and narrow chest of a monkey, yet capable of wide movement of the hip and thumb as in apes."
--Smithsonian Museum of Natural History

So Aegyptopithecus was ape-like monkey believed to be ancestral to Proconsul, a "monkey-like ape".

 

[Cirbryn]

Within thought systems, there are paradigm shifts. An analogous school of thought would be Newton's work on gravity and Einstein's Theory of Relativity. Newton's work is still useable but Einstein's work is more elegant.

Cladistics is a refinement of traditional taxonomy. It is more organic and thus reflects a biological system better. As to who uses it, it is better to be ahead of the curve of a paradigm shift than behind it.

The Theory of Relativity explains real life observations that previous theories couldn’t explain. Cladistic systematics doesn’t do that, it just involves an alternative means of classifying real life observations. It’s like fighting over whether to use the Dewey decimal system or the Library of Congress system. One system might be more useful than another in particular areas, but neither one actually explains real life observations.

Aron is implying to people that if they don't accept this alterative system they'll be unscientific. Is that true or not?

I am not sure that he is implying that.

From post 327: (quoting me) “I have no problem with you giving cladistics your best pitch, but you need to let them know that a non-cladistic (paraphyletic) interpretation of the term “monkey” (or any other such term) is perfectly acceptable among biologists, and that evolutionary theory is compatible with either viewpoint. Got any problems with that?"

And Aron’s response: “Yes, I have an enormous problem with that … paraphyly is not acceptible in taxonomy anymore ….”

So there’s the question. To know whether or not paraphyly is acceptable in taxonomy anymore, we have to look at the extent to which taxonomists currently use or allow paraphyly. It’s a question regarding the norms of use, not about some independent facet of the real world such as gravitational lensing or the advance of Mercury’s perihelion.

 

[Lilandra]

The Theory of Relativity explains real life observations that previous theories couldn’t explain. Cladistic systematics doesn’t do that, it just involves an alternative means of classifying real life observations. It’s like fighting over whether to use the Dewey decimal system or the Library of Congress system. One system might be more useful than another in particular areas, but neither one actually explains real life observations.

I am not sure then what you mean by real world observations. If what has been "observed" in the fossil record and comparative genomics are not real life observations, then what are they?

From post 327: (quoting me) “

I have no problem with you giving cladistics your best pitch, but you need to let them know that a non-cladistic (paraphyletic) interpretation of the term “monkey” (or any other such term) is perfectly acceptable among biologists, and that evolutionary theory is compatible with either viewpoint. Got any problems with that?"

And Aron’s response: “Yes, I have an enormous problem with that … paraphyly is not acceptible in taxonomy anymore ….”

So there’s the question. To know whether or not paraphyly is acceptable in taxonomy anymore, we have to look at the extent to which taxonomists currently use or allow paraphyly. It’s a question regarding the norms of use, not about some independent facet of the real world such as gravitational lensing or the advance of Mercury’s perihelion.

All right if it is a matter of whether paraphyly is acceptable or not in taxonomy, then it won't be difficult to answer this question.

Is there one common monkey characteristic in Simiiformes that evolved paraphyletically? It should be easy to name 2 species within the Greater Monkeys that evolved binocular vision for example independently.

I am talking about the real world where these traits evolved.

 

[Cirbryn]

Wrong, that wouldn't be an option, because in a cladistic system, the classification isn’t determined by the characters. The physical characteristics do define the phylogeny, but it is the phylogeny that determines the classification. That’s the only way that makes sense. Since it is impossible to evolve out of one’s ancestry, and a bit ridiculous for a change in descendants to redefine the parents, then it only makes sense to categorize the new example as adhering to all the fundamental descriptives of the parent clade –but with the additional alteration being used to further define the subset. For example, snakes can be said adhere to the total description of tetrapods (four-limbed stegocephalians) –in addition to the loss of limbs.

Sorry, that doesn’t work for me. Either all tetrapods have four legs or they don’t. We don’t have tetrapods slithering around that both have four legs and don’t have any legs. I do think you’re correct that the characters are used to build the phylogenetic tree, which then serves to indicate the clade. I just think it’s silly to pretend that therefore there must be characters that are constant throughout any particular clade. The characters of organisms before and after a branching are used to determine how the branching proceeded. We don’t have to assume the same characters used to determine a branching will still be present in the clade millions of years later. That’s the same thing I was talking about when you asked me how we’d figure out whether a newly discovered animal was a monkey and I said we’d look at where it fit into the known tree.

The ability to avoid worrying about characteristics common to the entire group could at times be an advantage of phylogenetic systematics over Linnaean, if the people supporting phylogenetic systematics would stop trying to pretend there must be such common characteristics for every clade. Linnaean taxa actually are defined by their common characteristics. That’s why some taxa need to be paraphyletic – because they’ve produced organisms that evolved to lose those characteristics. On the plus side of that, many of those common characteristics are important to note, and naming groups that share them allows us to talk about them more easily. I’ve already talked about the importance of the characteristic of gene flow, which defines Linnaean species. 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? Are you even allowed to utter such a paraphyletic name as that? It must be even more difficult for you to talk about mosasaurs, since so far as I know we don’t have clear evidence to show whether they gave rise to snakes (thus making them paraphyletic) or not. 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? 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?

In the Linnaean system, you have apes and humans and then have to find something half-way between them

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 – there’s 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. Numerous websites take the same approach. 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. Families, genera and species, on the other hand, are not used in a purely phylogenetic system.

FWIW, here’s what the book had to say about the reorganization: “The family Hominidae has until recently included only one living member, Homo sapiens, with the great apes being assigned to a separate family, Pongidae. However, recent data indicate a close relationship between humans and chimpanzees and necessitated a redefinition of the hominidae (Grove, 1989).

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

Similarly, if I say only “synapsids”, with no further qualifiers, it is usually going to be in a context that refers to the stem groups, and easy to understand if I’m referring to all modern mammalia as well. And if there were any potential for confusion, I could clarify that as simply as saying “basal” therapsids, “primitive” mammals, “early” hominids, or “non-avian” dinosaurs. Its much simpler than the Linnaean system where you actually have to know the names of the collectives before you can ask about them.

But you may need to be more specific than just “basal therapsids” or “non-avian dinosaurs”. Which basal therapsids? Isn't "basal therapsid" itself paraphyletic. Where to the "basal therapsids" stop and the "somewhat less basal therapsids" begin? 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. 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.

The Linnaean perspective is by its very nature incapable of accurately depicting evolutionary relationships because its construct is such that daughter groups aren’t part of their parent’s families, and siblings may not even be related.

Got any examples of sibling groups in the Linnaean system that aren’t related?

Clades are objectively verifiable, accurate renderings of real evolutionary relationships

Clades aren’t objectively verifiable in the sense that we can be sure a given phylogenetic tree is correct. They are subject to problems of convergent evolution just like everything else. At the species and lower level the trees of particular genes often do not agree with each other or with the actual genetic separation of the species. Phylogenetic trees are statistical best guesses and are often shown to be incorrect with additional data.

 

[Lilandra]

Frustrated, they replied that I "think too much."

I can't believe you managed to vex a Buddhist monk, for Pete's sake!

 

[Cirbryn]

I can't believe you managed to vex a Buddhist monk, for Pete's sake!

I can.

 

[Cirbryn]

I am not sure then what you mean by real world observations. If what has been "observed" in the fossil record and comparative genomics are not real life observations, then what are they?

Those are real life observations. I’m saying cladistic systematics doesn’t explain those observations any better than Linnaean systematics. They just organize the observations differently, like the Dewey system and the Library of Congress system organize books differently.

All right if it is a matter of whether paraphyly is acceptable or not in taxonomy, then it won't be difficult to answer this question.

Is there one common monkey characteristic in Simiiformes that evolved paraphyletically? It should be easy to name 2 species within the Greater Monkeys that evolved binocular vision for example independently.

Paraphyly means you group a bunch of related organisms so as to exclude some of their descendants. See the picture here where the blue area comprising class Reptilia excludes the class Aves (birds). In that example, Reptila is paraphyletic to Aves. Paraphyly doesn’t involve the independent evolution of a particular characteristic (such as binocular vision) in separate lines. Such independent evolution of characteristics does occur, and can play havoc with constructing phylogenetic trees, but that would more properly be described as a polyphyletic origin of a characteristic. Occasionally the polyphyletic origin of one or several characteristics causes us to mistakenly group the organisms themselves polyphyletically (meaning we include separate lineages in the group but leave out their common ancestors), but neither cladistic nor Linnaean systematics is any better at avoiding that. For example, both Linnaean and cladistic systems group all the toothed whales together as separate from the baleen whales, but recent genetic evidence indicates sperm whales are actually more closely related to the baleen whales than to the other toothed whales (John Avise, Molecular Markers, Natural History and Evolution, 2004). That means either sperm whales evolved teeth and echolocation independently of other toothed whales (polyphyletic origin of those characteristics), or that baleen whales started with teeth and echolocation and subsequently lost them both. Presumably, assuming the genetic tests are confirmed, the Linnaean whale taxa and cladistic trees showing whale evolution will both be reconfigured to take this new information into account.

 

[Lilandra]

Paraphyly means you group a bunch of related organisms so as to exclude some of their descendants. See the picture here where the blue area comprising class Reptilia excludes the class Aves (birds). In that example, Reptila is paraphyletic to Aves. Paraphyly doesn’t involve the independent evolution of a particular characteristic (such as binocular vision) in separate lines.

I do understand the distinction you are making between paraphyletic and monophyletic groups. The point I am making to you is that perhaps the reason paraphyly is not acceptable is because biological relationships are lost to make classification easier.

The reason I bring up shared characteristics is because monkeys did not evolve these traits independently. Monophyly reflects these biological relationships. Monkeys don't become so derived that they become another paraphyletic group Apes.

Such independent evolution of characteristics does occur, and can play havoc with constructing phylogenetic trees, but that would more properly be described as a polyphyletic origin of a characteristic.

That is not what I asked. I asked if any common characteristic of Greater Monkeys evolved independently. I am aware that certain environments favor certain characteristics in independent lineages.

If the answer is no, then monkeys are better classified as a monophyletic group.

Occasionally the polyphyletic origin of one or several characteristics causes us to mistakenly group the organisms themselves polyphyletically (meaning we include separate lineages in the group but leave out their common ancestors), but neither cladistic nor Linnaean systematics is any better at avoiding that. For example, both Linnaean and cladistic systems group all the toothed whales together as separate from the baleen whales, but recent genetic evidence indicates sperm whales are actually more closely related to the baleen whales than to the other toothed whales (John Avise, Molecular Markers, Natural History and Evolution, 2004). That means either sperm whales evolved teeth and echolocation independently of other toothed whales (polyphyletic origin of those characteristics), or that baleen whales started with teeth and echolocation and subsequently lost them both. Presumably, assuming the genetic tests are confirmed, the Linnaean whale taxa and cladistic trees showing whale evolution will both be reconfigured to take this new information into account.

This is all very fascinating but doesn't address the question. Additionally, cladistics can be adjusted to reflect the sperm whale's relationship to baleen whales. Cladistics does not ignore genetic information. Most importantly, if a species of monkey is shown to have come by a monkey characteristic independently then it will be reclassed. The entire monkey tree won't be up rooted.

 

[Cirbryn]

I do understand the distinction you are making between paraphyletic and monophyletic groups. The point I am making to you is that perhaps the reason paraphyly is not acceptable is because biological relationships are lost to make classification easier.

The reason I bring up shared characteristics is because monkeys did not evolve these traits independently. Monophyly reflects these biological relationships. Monkeys don't become so derived that they become another paraphyletic group Apes.

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. Assuming apes evolved from monkeys, the apes did indeed become so derived that they formed another group (which is monophyletic), thereby making monkeys paraphyletic.

That is not what I asked. I asked if any common characteristic of Greater Monkeys evolved independently. I am aware that certain environments favor certain characteristics in independent lineages.

If the answer is no, then monkeys are better classified as a monophyletic group.

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.

 

[Cirbryn]

You hadn’t “explained” that you always make clear to others that you are speaking non-paraphyletically.

Yes I did -frequently.

Such as?

I’m glad to hear that you do typically clarify that. The only remaining point, discussed below, is the extent to which you imply that scientists in general only use such non-paraphyletic definitions.

I cited numerous examples where this is not the case, and that it is indeed sad that it is not.

I’m 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 isn’t.

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

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

Being a reality-based argument, even if I were in a distinct minority, I would still be able to demonstrate the validity of my claim regardless what the majority perspective is, or what the authorities prefer to teach.

Let me explain something about my own iconoclast perspective, and how I see that relating to this conversation. A few months ago, I went the Buddhist temple here in Dallas. I both love and loath Buddhist philosophy. One of my problems with it is that he temple's teacher, (pictured with me below) taught us that Buddhism is atheist -even though he admitted that tens of millions of Buddhists do worship Shakyamuni as a god, and even those who don't still consider him an immortal being with miraculous powers who hears our prayers, and isn't that what a god is? He also said Buddhists had no faith, but he admitted they believe what they do in lieu of any demonstrable evidence. Isn't that what faith is?

<snip>

The point is, authority opinion can be wrong -even if there is a universally-held concensus. Whatever is really true is not determined by popular vote; it is determined by analysis of the facts. And that's where I'm coming from when I say that humans are monkeys. I don't mean humans are monkeys according to ...anyone. I mean humans are demonstrably monkeys whether anyone wants to admit that or not. It appears to be, regardless whether you're referring to the Linnaean or phylogenetic systems, that humans are monkeys by definition. But more importantly, they are monkeys by derivation -regardless what system you use or what the "accepted standard" is, or what the 'authority consensus" happens to be.

Your argument above relies on the existence of commonly held definitions of atheism, religion, faith, etc. You’re saying they may not claim to be a religion, but they meet the accepted definition so that means they are one anyway. The claim only carries weight for people who agree with you regarding those definitions. Your argument about monkeys relies on the same kind of thing: in this case the idea that a taxonomic group must be monophyletic to be valid. But there’s no support for that – it’s a matter of opinion – and one that most taxonomists probably do not share.

There are places in Idaho where you can go due west and lose an hour (see here) (so you’d go from 3:00 to 4:00 for instance). This despite the fact that the sun rises in the east and sets in the west. Shall I call up the authorities and let them know their system is objectively wrong, since at any one time the sun will always be closer to setting as viewed from the east than it is as viewed from the west? I suspect they’d tell me they don’t care. Shall I instead just start telling everyone I meet in the area that it’s really 3:00 and not 4:00? Let’s hope no one is foolish enough to believe me if I do.

 

[Lilandra]

Since I don&#8217;t agree that paraphyly is unacceptable,

Why because paraphyly is still in use?

I&#8217;m not in a position to speculate as to why it would be. Paraphyly isn&#8217;t meant to reflect polyphyletic characteristics though. It is meant to reflect the presence of characteristics (either ancestral or derived) that aren&#8217;t present in the rest of the clade.

I thought I was talking about groupings that include the common ancestor-monophyly. Polophyly according to Wiki is...

a taxon is polyphyletic (Greek for "of many races") if the trait its members have in common evolved separately in different places in the phylogenetic tree.

Like the marsupial mammal Tasmanian wolves and placental mammal wolves. An equivalent in monkey terms would be a hypothetical marsupial monkey and a placental monkey. I don't think that among any of the known monkey species there is one that can't be phylogenetically placed among monkeys.

It would be sort of cool if there was another race of humans that developed independently with close common ancestry with tamarins instead of chimps, They would be like the Lilliputians from Gulliver's Travels.
That would be polyphyly.

Cladistics ignores such characters, so cladistics ignores biological information (and in the case of speciation, biological relationships) to make classification easier.

I don't think speciation is ignored in cladistics.

 

[Cirbryn]

Since I don&#8217;t agree that paraphyly is unacceptable,

Why because paraphyly is still in use?

I don&#8217;t agree that it&#8217;s unacceptable generally because taxonomists generally accept it (so it&#8217;s still in use). I don&#8217;t personally find it unacceptable because paraphyletic groupings can convey important biological information that would be lost if all groups were required to be monophyletic.

Paraphyly isn&#8217;t meant to reflect polyphyletic characteristics though. It is meant to reflect the presence of characteristics (either ancestral or derived) that aren&#8217;t present in the rest of the clade.

I thought I was talking about groupings that include the common ancestor-monophyly. Polophyly according to Wiki is... &#8220;a taxon is polyphyletic (Greek for "of many races") if the trait its members have in common evolved separately in different places in the phylogenetic tree.&#8221;
Like the marsupial mammal Tasmanian wolves and placental mammal wolves. An equivalent in monkey terms would be a hypothetical marsupial monkey and a placental monkey. I don't think that among any of the known monkey species there is one that can't be phylogenetically placed among monkeys.

It would be sort of cool if there was another race of humans that developed independently with close common ancestry with tamarins instead of chimps, They would be like the Lilliputians from Gulliver's Travels.
That would be polyphyly.

I agree that would be polyphyly. I thought we were talking about paraphyly.

Cladistics ignores such characters, so cladistics ignores biological information (and in the case of speciation, biological relationships) to make classification easier.

I don't think speciation is ignored in cladistics.

If you require that all groups be monophyletic (and thus include all descendants), how are you going to represent the relationship of a parent species to a daughter? You&#8217;d have to suggest, as the PhyloCode apparently does, that the daughter should still be considered part of the parent. Thus you lose the information that the daughter species is no longer exchanging genes with the parent and has embarked on its own unique evolutionary path. In paleobiology that&#8217;s not so much of a problem because generally it isn&#8217;t clear what the exact parent species was anyway. But avoiding the problem isn&#8217;t solving it.

Additionally, we can now produce lots of great cladograms of living species and subspecies based on genetic data, but that genetic data often fails to reflect speciation events, and also indicates both paraphyly and polyphyly within species at the genetic level.

For instance, it&#8217;s hardly clear that polar bears are a separate species from all the various intraspecific clades of brown bears in the above cladogram from Avise 2004 (Molecular Markers, Natural History, and Evolution), at 291. The position of polar bears on the cladogram could be due to limited interbreeding in the past, but it also could be due to the fact that a new species doesn&#8217;t immediately get a bunch of new DNA. It inherits its DNA from some subportion of the parent species.

This figure from the same book shows how the selection of the individuals going into the new species can leave that species paraphyletic or polyphyletic for the particular DNA being tested. Presumably, the polar bear situation would have been similar to situations C or D.

This figure shows the percentages of paraphyly found in various classes of animal species for mitochondrial DNA.

As the DNA in the parent and daughter species evolve in independent directions, eventually the paraphyly and polyphyly indicated by such DNA disappears. The above graph indicates how long that can take, assuming no stabilizing selection.

So while I agree with you that cladistics doesn&#8217;t assume speciation doesn&#8217;t happen, I think it has a hard time accurately reflecting the relationships that speciation produces. It would have an even harder time if all paraphyletic groups were disallowed. Not only is paraphyly still in use, we couldn't get along without it.

 

[Lilandra]

If you require that all groups be monophyletic (and thus include all descendants), how are you going to represent the relationship of a parent species to a daughter? You’d have to suggest, as the PhyloCode apparently does, that the daughter should still be considered part of the parent. Thus you lose the information that the daughter species is no longer exchanging genes with the parent and has embarked on its own unique evolutionary path. In paleobiology that’s not so much of a problem because generally it isn’t clear what the exact parent species was anyway. But avoiding the problem isn’t solving it.

You'll have to forgive me if at times I seem dense. I have only taken in interest in learning more about Biology in the past year and a half after getting whupped (sp.)as an OEC here. Whatever new thing I learn about I am grateful for.

I am not certain from what I understand of the Phylocode that daughter groups are lost to monophyly.
This is Wiki's description...

PhyloCode is a draft for a formal set of rules governing phylogeneticnomenclature. Its current version is specifically designed to regulate the naming of clades, which do not have set ranks, unlike conventional Linnaean taxonomy.
In PhyloCode, a clade name may be defined in one of the following manners (not exhaustive):

1. Node-based: "the least inclusive clade containing the species or organisms A, B, ..."
2. Branch-based: "the clade consisting of A and all organisms or species that share a more recent common ancestor with A than with Z"
3. Apomorphy-based: "the clade stemming from the first organism or species to possess the apomorphy (unique character) M as inherited by A"

From what I see it looks as though there are different groupings or clusters to choose in constructing a cladogram. Node based looks to be comprised of species.

Additionally, we can now produce lots of great cladograms of living species and subspecies based on genetic data, but that genetic data often fails to reflect speciation events, and also indicates both paraphyly and polyphyly within species at the genetic level.

But this cladogram names the species of Brown bear. The info is still there.

For instance, it’s hardly clear that polar bears are a separate species from all the various intraspecific clades of brown bears in the above cladogram from Avise 2004 (Molecular Markers, Natural History, and Evolution), at 291. The position of polar bears on the cladogram could be due to limited interbreeding in the past, but it also could be due to the fact that a new species doesn’t immediately get a bunch of new DNA. It inherits its DNA from some subportion of the parent species.

This is interesting because it would seem that polar bears are not that distantly related from brown bears to be considered paraphyletic.
Check this story out...


This is a grizzly/polar hybrid shot in Canada in May. There had been rumored sightings of strange looking hybrids but this is the first confirmed hybrid in the wild. They had been paired in zoos before with fertile offspring. I think people were not certain whether the 2 would still mate in the wild because of speciation and they occupy different ecological niches.

But there you are the cladogram is reflecting brown bear relationships.
http://msnbc.msn.com/id/12738644/?GT1=8199

This figure shows the percentages of paraphyly found in various classes of animal species for mitochondrial DNA.

As the DNA in the parent and daughter species evolve in independent directions, eventually the paraphyly and polyphyly indicated by such DNA disappears. The above graph indicates how long that can take, assuming no stabilizing selection.

in this sense, paraphyletic groups are not useless. They note compiled derived characteristics in daughter groups.

But why it an either/or situation? Don't most organisms still share a percentage of nuclear DNA similarity even if mtDNA traceability disapears?

 

[Aron-Ra]

I don’t agree that it’s unacceptable generally because taxonomists generally accept it (so it’s still in use). I don’t personally find it unacceptable because paraphyletic groupings can convey important biological information that would be lost if all groups were required to be monophyletic.

Like the fact that apes descend from monkeys rather than monkey-like non-monkeys? You tradition excels at hiding information under the rug on purpose.

If you require that all groups be monophyletic (and thus include all descendants), how are you going to represent the relationship of a parent species to a daughter?

Just the way I've explained to you nearly a dozen times now; mark the emergence of the new characteristic without pretending that some of the old family trees you subjectively choose stop where the new family trait begins.

You’d have to suggest, as the PhyloCode apparently does, that the daughter should still be considered part of the parent. Thus you lose the information that the daughter species is no longer exchanging genes with the parent and has embarked on its own unique evolutionary path.

No no no. As I've told you several times before, with monophyly, you retain all the information of the parent clade, and all the information for each divergence in it, including the addition of the trait you're trying to point out here. Don't limit all your conversations to species only. We're talking about whole family trees here.

In paleobiology that’s not so much of a problem because generally it isn’t clear what the exact parent species was anyway. But avoiding the problem isn’t solving it.

How ironic that you would say that. I might as well just write one response to you and cut-and-paste it into this thread every day because I keep telling you the same things overand over again only to see you show no knowledge of it tomorrow.

Additionally, we can now produce lots of great cladograms of living species and subspecies based on genetic data, but that genetic data often fails to reflect speciation events, and also indicates both paraphyly and polyphyly within species at the genetic level.

Linnaean taxonomy fails to log speciation events. But with clades, it is possible to trace a lineage both on paper and in real life. Common ancestry, by definition, demands a monophyletic -such as you have illustrated here:

And here:

This figure from the same book shows how the selection of the individuals going into the new species can leave that species paraphyletic or polyphyletic for the particular DNA being tested. Presumably, the polar bear situation would have been similar to situations C or D.

Its only paraphyletic or polyphyletic depending on what names you choose to give each group. If you say that snakes aren't lizards anymore, then they're paraphyletic. If you say they're still Squamates but without legs, then they're monophyletic. But neither you or I have changed their genetic structure in our disagreement. So either paraphyly means something as yet undiscussed in this thread, or its determination depends on an assumption of convention.

This figure shows the percentages of paraphyly found in various classes of animal species for mitochondrial DNA.

Hybridization can't cause children to not be part of their parent's families anymore. Nor has there ever been any fundamental difference between ancestors and thier descendants at any point in evolutionary history that I am aware of. Nor can the same taxon emerge independantly from two different ancestors unrelated to each other. Care to explain how this similation implies otherwise?

As the DNA in the parent and daughter species evolve in independent directions, eventually the paraphyly and polyphyly indicated by such DNA disappears. The above graph indicates how long that can take, assuming no stabilizing selection.

So even your similation reveals a single common ancestor. This is my instructors taught me that evolution actually promotes, including one who was a geneticist with the human genome project:

"The evidence of taxonomic relationships is overwhelming when you look at the comparisons between the genomic (DNA) sequences of both closely-related and even distantly-related species. The DNA of yeast and humans shares over 30% homology with regard to gene sequences. Comparison of the human and mouse genome shows that only 1% of the genes in either genome fails to have an orthologue ithe other genome. Comparison of non-gene sequences, on the other hand, shows a huge amount of divergence. This type of homology can be explained only from descent from a common ancestor."
--Jill Buettner, professor of Genetics at Richland College, Dallas, TX

And I showed you the Shape of Life project, another remarkable and nationally publicized genetic research endeavor where they traced all of 'Animalia' to a single monophyletic source. But you just sort of skipped over that without mention.

So while I agree with you that cladistics doesn’t assume speciation doesn’t happen, I think it has a hard time accurately reflecting the relationships that speciation produces. It would have an even harder time if all paraphyletic groups were disallowed. Not only is paraphyly still in use, we couldn't get along without it.

Yes we can, because it serves no value but to create confusion. Where there is any difference between these methods, monophyletic groups are easier, and as that is the way all things evolve anyway, it is the more realistic convention.

 

[Aron-Ra]

Since it is impossible to evolve out of one's ancestry, and a bit ridiculous for a change in descendants to redefine the parents, then it only makes sense to categorize the new example as adhering to all the fundamental descriptives of the parent clade –but with the additional alteration being used to further define the subset. For example, snakes can be said adhere to the total description of tetrapods (four-limbed stegocephalians) –in addition to the loss of limbs.

Sorry, that doesn't work for me.

Then you’re not only ignoring the wealth of characters which establish these classifications, but you’re missing the whole point of taxonomy as well. I don't know what Linnaeus' motivation was in the days before Darwin. But now that we know about evolutionary relationships, there is only one reason to do taxonomy at all, and that is to try and trace evolutionary phylogenies. That means you mark where the body plans of Stegocephalians were adapted for four limbs, you identify where that branch with a name and that name has to apply to everything on that branch. It doesn't matter one iota if those characters are retained by every stem down that branch. If they are lost again later on, that would mark a new clade still on the same branch! If you're not trying to figure these relationships out, then why would you even care about taxonomy in the first place? What other function can it serve?

Either all tetrapods have four legs or they don't.

What about cetaceans?

We don't have tetrapods slithering around that both have four legs and don't have any legs.

What about Sirenians?

I do think you're correct that the characters are used to build the phylogenetic tree, which then serves to indicate the clade. I just think it's silly to pretend that therefore there must be characters that are constant throughout any particular clade.

Then why are you still arguing this with me? Snakes are at once members of Stegocephalia (characterized by having digits on their limbs) Tetrapoda, (adapted to four limbs) and Anthracosauria (having five digits on their limbs.) None of these traits are still present in snakes, and most of them are missing on horses too, who are also in both of those same groups. But then, none of these clades are identified only by those traits, and the only thing that really matters is what the evolutionary relationships are.

The characters of organisms before and after a branching are used to determine how the branching proceeded. We don't have to assume the same characters used to determine a branching will still be present in the clade millions of years later.

If having "four-limbs" doesn't have to be constant throughout the whole clade, then why do you insist on removing everything that doesn't retain four limbs?

That's the same thing I was talking about when you asked me how we'd figure out whether a newly discovered animal was a monkey and I said we'd look at where it fit into the known tree.

No it is not the same thing. Because in that case, we still fit every character indicative of monkeys –including the fact that we have five digits on each of our four limbs. One of the characters which specify apes, (at least the 'great' apes) is that we have a broader chest than others in that lineage. You want to turn that around backwards and try to claim that monkeys have a narrower chest than apes. But you've failed even in that because Proconsul has the narrow rib cage you're talking about, and earlier monkeys had five-cusped molars, and everything else you want to try to use to keep us apart. Its not going to work. Every character trait indicative of all monkeys collectively is also descriptive of apes and still applies to humans. And (as I said before) once you isolate what kind of monkey it is, if you discover that it is an ape, then you've still identified what kind of monkey it is. Being an ape doesn't make it a non-monkey classification. It becomes a certain type monkey specification.

The ability to avoid worrying about characteristics common to the entire group could at times be an advantage of phylogenetic systematics over Linnaean, if the people supporting phylogenetic systematics would stop trying to pretend there must be such common characteristics for every clade.

Since we obviously don't, then maybe it is you who should stop all this "silly pretending" that we do.

Linnaean taxa actually are defined by their common characteristics. That's why some taxa need to be paraphyletic – because they've produced organisms that evolved to lose those characteristics.

Then, by your own admission, you "fail to reflect" important information from an evolutionary perspective, and you do so deliberately.

On the plus side of that, many of those common characteristics are important to note, and naming groups that share them allows us to talk about them more easily. I've already talked about the importance of the characteristic of gene flow, which defines Linnaean species.

Cladistics uses the same definition –where that applies to animals. So there is no specifically 'Linnaean' definition.

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?

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

"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.

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

I can say anything I want, as long as it is understood what that means. For example, 'monkey' always means 'anthropoid', where 'fish' may mean 'chordate', and 'reptile' may mean 'Diapsid', (in which case, both still apply to birds) or these words may not be meaningful at all anymore. One only needs to be clear in context.

It must be even more difficult for you to talk about mosasaurs, since so far as I know we don't have clear evidence to show whether they gave rise to snakes (thus making them paraphyletic) or not.

It wouldn't be difficult for me to talk about Mosasaurs either way, since the original idea was never that snakes evolved from within their group, and it is now known that they did not, as indicated by the snake with legs that I already showed you. However, if snakes had emerged from within the Mosasaur clade, then snakes would be legless mosasaurs today.

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?

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.

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?

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

 

[Aron-Ra]

In the Linnaean system, you have apes and humans and then have to find something half-way between them

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 – there's 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.

Which explains the revision.

Hominidae was presented as a family, not a clade. Genera and species within the family were discussed.

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

Numerous websites take the same approach.

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

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.

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.

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

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.

FWIW, here's what the book had to say about the reorganization: "The family Hominidae has until recently included only one living member, Homo sapiens, with the great apes being assigned to a separate family, Pongidae. However, recent data indicate a close relationship between humans and chimpanzees and necessitated a redefinition of the hominidae (Grove, 1989). 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.

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.

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

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

Thus exhibiting yet another failure of the Linnaean system,

one commonly exploited by all of evolution's critics.

 

[Aron-Ra]

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.

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 isn’t 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.

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. 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. 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!

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.

 

[Aron-Ra]

Similarly, if I say only "synapsids", with no further qualifiers, it is usually going to be in a context that refers to the stem groups, and easy to understand if I'm referring to all modern mammalia as well. And if there were any potential for confusion, I could clarify that as simply as saying "basal" therapsids, "primitive" mammals, "early" hominids, or "non-avian" dinosaurs. Its much simpler than the Linnaean system where you actually have to know the names of the collectives before you can ask about them.

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

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

Isn't "basal therapsid" itself paraphyletic.

No.

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

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.

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.

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.

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.

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.

The Linnaean perspective is by its very nature incapable of accurately depicting evolutionary relationships because its construct is such that daughter groups aren't part of their parent's families, and siblings may not even be related.

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

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.

Clades are objectively verifiable, accurate renderings of real evolutionary relationships

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

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.

They are subject to problems of convergent evolution just like everything else.

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.

At the species and lower level the trees of particular genes often do not agree with each other or with the actual genetic separation of the species. Phylogenetic trees are statistical best guesses and are often shown to be incorrect with additional data.

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.