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Re: BAD vs. BADD (was: Re: Most popular/common dinosaur misconceptions)

While I am well aware of the fact that PN can be
removed in favour of a more rank based system in a
cladistic analysis, I know of no case where the roles
were reversed. That is to say, when has PN ever been
used without cladistics (i.e. naming a traditional
Linnean tree using PN)?

Apart from DA (thanks for reminding me!), I'm not aware of a case. I suppose cladistics is just too widespread nowadays.

Well, for one, birds locomote in a manner completely
different from those of dinosaurs (classic dinosaurs).

Check again where on the tree that change happened. Anywhere but close to *Archaeopteryx*.

Dinosaurs probably didn't see like birds
either; with relatively fixed eyes that require head
bobbing in order to walk effectively.


Would this be determinable in fossils at all?

In all honesty the only grey area that I've ever seen
with birds and dinosaurs involves a small set of
maniraptors and very early, (archaeopterigiformes and
such) birds.

What about teeth? What about bipedality? If the grey area is everything between Crocodylia and Neornithes, it is very broad!

Ah, no, we're not back to the days of Lamarck and
Jussieu. Life is not a continuum (points on a
one-dimensional line), it is a tree; almost all
imaginable lines between any two organisms cross a
very real gap.


If this is true, then why do I see Jaime and others
arguing that there is no gap?

Because I wasn't clear enough. :-) Along those "lines between imaginable organisms" that stay inside the branches of the tree there are no gaps. If you jump directly from twig to twig, you have to cross gaps almost always.

Quick aside: it should be pointed out that Lamarck did
view the evolution of life as a tree, and not a
straight line ladder arrangement. This occurred later
in his life, but was still published.


Ah.

I've only seen them go up to superfamily (Iguania,
Scleroglossa), but I'm not sure if they've ever gone
further. I know they still accept order Squamatas, if
that counts.

If they explicitely call it an order, it certainly counts. (However, Iguania and Scleroglossa are not superfamilies, as shown by the fact that they aren't called Iguanoidea and Lacertoidea!)

Why is it okay to call "birds" dinosaurs, but it's not
okay to call snakes "lizards?" It just seems like a
double standard to me.

Why? Once you have the vernacular on the one side, once on the other. Besides, what's the real difference between "birds" and "Aves"?

I'd say that dinosaurs, for the most part, were
generaling adapting to various niches as large
terrestrial animals.

I submit that the birds were the only ones able to get around the mammalian competition (by flying around it). What exactly "bird" means here, however, has yet to be determined...

I'd hesitate from
separating them as a class just because they still
retain many of the key features that unite mammals
(the inner ear bones, suckling, etc).

This is where it becomes interesting. If you insist on the inner ear bones, mammals are diphyletic -- in Ausktribosphenidae, those bones were still in the lower jaw.

The others don't appear to be as derived away from
Mammalia in general, as cetaceans (even bats still
retain fur, the inner ear bones, and still suckle
their young).

If you don't insist on the inner ear bones, you better come up with (yet another) new criterion to tell if *Tritheledon* is a mammal.

There's nothing wrong with insisting on a character (keyword: apomorphy-based definition), but insisting that it cannot be lost asks for unnecessary problems.

Snakes don't warrant a separate status just because
they are limbless. It's the huge changes to their
skull that matters more. Most limbless lizards all
retain relatively fixed skulls. This limits the type
of prey they can subdue, and thus their overall size.
Snakes evolved the most maleable skull ever seen in
tetrapods (as far as we know). This allowed for
greater prey choice, and far greater niche
expandability.

So I submit Order Macrostomata. Clearly scolecophidians and boas, let alone madtsoiids, are lizards; their skulls are just not flexible enough for me* to count.

* That's right. Me. The utter subjectiveness of Linnaean nomenclature leads to everyone making their very own classifications. Show me any two textbooks that use exactly the same! And if you manage to do that, show me any two papers from the primary literature that do! Even from the same author, provided they are more than, say, 5 years apart.

The only lizards that ever came close
to following snakes were pygopodids. Though they are
interesting, they still lag far behind in terms of
diversity and size range.


Isn't this an artefact of being stuck in Australia and lacking venom?

You keep arguing the semantics, but seem to be missing
my point. No one goes around using these "non-"
monikers anywhere but in vertebrate paleontology

Just a few days ago I saw a quite long-winded non-phrase that described some angiosperms. It's spreading -- in English, that is.

Perhaps if there was a more varied vocabulary in the
terms, this "non-" stuff wouldn't be so bothersome.
Still, after seeing all the examples given, I'd still
think it would be easier to say "dinosaur,"
"theropod," "maniraptor." etc.

Why privilege some paraphyletic groups over all others? Every study will need different paraphyletic groups (if any). "Flighless dinosaurs" would still be required under both systems; "toothed theropods" would even have to be doubled into "toothed theropods and toothed birds".

Better yet, look what happened to
"rhynchocephalia." That name wasn't dumped

Stop right here. I've seen it used more often than Sphenodontida, always for a clade that includes *Sphenodon* and *Gephyrosaurus* but not the squamates (...let alone the rhynchosaurs that were included in classical times).

There is logic in the old rank system. It provides a
nice, relative, guage of how far apart different
animals are.

It would be nice if phenetics actually worked. But it doesn't. Moreover, "evolutionary systematics" was never meant to be phenetics -- it was meant to be a weird compromise between phenetics and cladistics; for example polyphyletic groups are always dissolved as soon as they are recognised as such.

That there is no rigorous and
standardized definition of what constitutes a family,
order, or class, is a problem.


That's an understatement. :-)

I do think it could be fixed if there were enough
people willing to devote the time to it.

Then phenetics would have worked. (And this would still not have been enough -- see above.)

That said, having a relative guage of
separation is helpful. For instance if one told me
that _Spinosaurus_ was an offshore of some
crocodyliforme lineage, than I could be able to test
that simply by looking at the ranks. _Spinosaurus_ is
in the family Spinosauridae, which is in the order
Saurischia, which is in the class (for all intents and
purposes) Dinosauria. Crocodyliformes are in the
"class" Crurotarsi (again, for all intents and
purposes). So right off the bat, I know that
_Spinosaurus_ is probably not an offshoot of the
crocodyliformes because it differs all the way at the
"class level." To do the same thing using PN is
harder. In order to test the validity of _Spinosaurus_
is a crocodyliforme offshoot, I have to see where
clade Spinosauridae is, and how many clades away from
clade Crurotarsi that is. So right off the bat I need
a cladogram to answer my question (which is done in
cartoonish example so as to get the point across).

So what? Isn't a tree -- a picture -- easier to understand than a classification -- plain text?

Additionally, you need a tree anyway to make the classification in the first place.

I don't understand why you write you have to see "how many clades away from clade Crurotarsi that is". I don't understand what you mean. All you have to figure out is that *Spinosaurus* is not a member of Crurotarsi. You don't need any ranks for that.

Clade names might remain static, but clade membership,
and relationship with other clades does not.

That's a mighty improvement over the Linnaean system, where neither membership nor outgroup relationships nor the name nor the status as monophyletic vs paraphyletic need to stay constant!

For instance, if some paleontologist somewhere discovered
that _Spinosaurus_ and its kin actually had
crurotarsal ankles, and a few dozen other features
that would link it with Crurotarsi (which were
"remodeled" during evolution towards a theropod mimic
lifestyle), then Spinosauridae would still contain all
its current members, but the clade would have hopped
all the way into Crurotarsi. So no cladogram, means no
way of answering the question.

You said "lineage". This means you want a phylogenetic tree. You are not asking about nomenclature at all, you are asking about phylogenetics and nothing else!

Now suppose that someone made a Linnaean classification where, in spite of the abovementioned discovery, spinosaurids would stay dinosaurs. Dinosauria would be diphyletic, and the guy who'd tell you that *Spinosaurus* were some offshoot of some crocodyli...form lineage would most likely be right, in spite of the classification arguing otherwise (if MISTAKENLY interpreted as saying anything about phylogeny)!!! You are making quite a strawman out of Linnaean nomenclature. That's amazing. :-)

Long story short, as a disparity guage, the Linnean
rank system tends to work very well.


It tends not to work at all.

Speaking of, I completely missed another useful
example of an arbitrary system. This one was right
under my nose, in the other half of our field. How
about lithostratigraphic classification.

This is a very good example. <rubbing hands, putting on evil grin> Compare body stratotypes and boundary stratotypes.
Body stratotypes work, AFAIK, like this: "this is typical Maastrichtian rock (with a typically Maastrichtian fossil assemblage etc. etc.), and everything not too far above and below it is Maastrichtian". I get to decide what "not too far" means. Result: if my favourite enemy publishes a paper "wow, I've found a major extinction event at the X-Y boundary!", I can publish a reply "rubbish, the alleged event happened 3 million years before the boundary; the boundary itself was completely quiet", we are both right and both wrong. Just like Linnaean nomenclature: although you will hardly find it mentioned anywhere, Spinosauridae is defined as "the family that *Spinosaurus* belongs to", in other words, "everything that is not too distantly related to, and not too dissimilar from, *Spinosaurus*". Here, too, I get to decide what all that means. Result: splitting and lumping till the cows come home.
Boundary stratotypes are different: boundaries are defined (golden spike and all), so the Maastrichtian is everything between the Campanian-Maastrichtian and the Maastrichtian-Danian boundaries. No more non-discussions like the above. You'll have noted that two boundary stratotypes are needed to define one time slice, just like at least two anchors (specifiers) are needed for a phylogenetic definition.

There are MORE differences between bats
morphologically (and apparently genetically as well)

The genetic ones might be countable. The morphological ones are neither countable nor measurable -- see phenetics.

I have a problem with separating bats partly because
bats make up the majority of mammal species alive
today (and probably in the past as well). It would
almost seem easier to call bats mammals, and other
mammals something else.

Eh, you forgot the rodents. There are still more rodents than bats out there.

That aside, the standard definition of a mammal was
based on fur, suckling and the three inner ear bones.


_Sometimes_.

I've seen the petrosal or something used instead (the fusion of pro- and opisthotic) so that *Adelobasileus*, known from an isolated braincase, was able to be the oldest and basalmost mammal.

Since Darwin, the traditional cutoff has been
_Archaeopteryx_. Personally I'd have gone closer to
the split between Enantiornithines and Neornithines
(where substantial differences between "classic"
dinosaurs occurs),


Which?

but it seemed to have been decided
long ago that a single character was more important
than a suite.

Suites are always temporary. They are nothing but ignorance that will go away once we find a fossil that has some but not all of those characters. This has happened with mammals, whales, tetrapods, birds, crocodiles... I think snakes are next :-)

So for better or for worse,
_Archaeopteryx_ seems to be it.

So, Sereno's node-based phylogenetic definition? The MRCA of *Archaeopteryx lithographica* and *Passer domesticus* plus all its descendants?

For snakes, the cut
lies in the skull and when it reached a specific
degree of kinesis. Yes, regardless the cut will be
arbitrary, but as I and others on this list have tried
to point out, it still remains useful.

1. Unless you fix it by means of an apomorphy-based phylogenetic definition, everyone will use their own "specific degree".
2. Unlike in phylogenetic nomenclature, such cutoffs cut both ways in Linnaean nomenclature. Recognising Serpentes as a suborder within Squamata prevents you from recognising Ophidia _at all_, and vice versa.

I do think a
standard measure of differences would make this form
of classification more rigorous, and helpful.


As I said: it would be a step forward if phenetics actually worked.

Youc can change the boundary, but you'd have to
publish your findings and see if they are agreed upon.
This has been occurring in science for decades. How
many taxonomic revisions are out there that were done,
but never took hold. How many new genus, or species
names were coined, that were ignored by the others.
All this was still done scientifically. The scientists
in question had to prove the validity behind their
thinking.


You wish.

I wish! But neither was it attempted in most cases, nor was it possible. Ranks are not defined, nor is there a criterion for which paraphyletic groups to recognise and which not -- or even for which clades to recognise and which not.

the end result still depended on the
will of the scientific masses to accept the new terms.

Commonly the scientific masses split 50/50 or 40/60 or 30/70, resulting in the consistent use of two or more mutually exclusive alternatives over decades or even centuries.

I'm not sure what those two taxa were doing exactly. I
haven't heard any real talks about _Microraptor_ being
an active flapper (vs. gliding), and _Caudipteryx_ was
showy, but earthbound. At least, that what it seems.
In some ways there were definitely following the
direction that birds took, but at a couple dozen
million years late, they obviously weren't going the
exact same way.


All this doesn't answer the question, which was

> Again, in what way were Microraptor and Caudipteryx going in the "same > direction" as Brachiosaurus and Triceratops rather than in the "same > direction" as Archaeopteryx and Jehlornis?

On the details, I'd like to mention that I don't believe in gliding theropods that aren't descended from active fliers, *Caudipteryx* may well be secondarily flightless, and the origin of flight may well be closer to the origin of Maniraptora than to that of (*Archaeopteryx* + Neornithes).

For this case, I would consider the radiation that
occurred among birds once they did "officially" become
Aves.

Which radiation? That of Ornithothoraces? That of Neornithes? That of Neognathae? That of Neoaves? That of Coronaves?

So I'd say diversity should matter as a
criterion for a name change. I know that will probably
gain some scour, since we only have the fossilized
remains of dinosaurs to compare with it.

That's just the practical problem. I'll tell you the theoretical one: There are 20,000 species of grasshoppers -- traditionally an order at most --, and 17,000 species within one family of beetles. (Or at least there were when I heard about them! Several thousand new insect species are described every year, with the only limitations being the number of entomologists in the world and the number of hours in a day.) Are you willing to sink all of Mammalia, no, Theropsida into a single family? I didn't think so. Are you willing to expand that beetle family into a class or superclass, rendering Coleoptera, I don't know, a kingdom? Didn't think so either.