On Tuesday, September 14, 2021 at 12:41:28 AM UTC-4, John Harshman wrote:
> On 9/13/21 8:09 PM, Peter Nyikos wrote:
> > On Monday, September 13, 2021 at 3:04:02 PM UTC-4, John Harshman wrote:
> >> On 9/13/21 11:39 AM, Peter Nyikos wrote:
> >>> On Monday, September 13, 2021 at 10:46:07 AM UTC-4, John Harshman wrote:
> >>>> On 9/13/21 6:32 AM, Peter Nyikos wrote:
> >>>>> On Friday, September 10, 2021 at 11:57:10 PM UTC-4, Glenn wrote:
> >>>>>> On Friday, September 10, 2021 at 6:57:32 PM UTC-7, Peter Nyikos wrote:
> >>>>>>> Carcharodontosauria (shark-toothed saurians) were the last of the
> >>>>>>> allosaurids, found in Laurasia up to the end of the Turonian
> >>>>>>> (early Late Cretaceous) but surviving in Gondwana to the end of the Cretaceous.
> >>>>>>> In a role reversal from what I've been accustomed to, the largest of these allosaurids
> >>>>>>> were considerably larger than the largest tyrannosauroids of the time.
> >>>>>>>
> >>>>>>> The "new" find is actually a rediscovery:
> >>>>>>>
> >>>>>>> "The chunk of jawbone was found in Uzbekistan's Kyzylkum Desert in the 1980s, and researchers rediscovered it in 2019 in an Uzbekistan museum collection."
> >>>>>>> https://www.microsoftnewskids.com/en-us/kids/animals/gigantic-shark-toothed-dinosaur-discovered-in-uzbekistan/ar-AAOhazl?ocid=entnewsntp
> >>>>>>>
> >>>>>>> The chunk is a partial maxilla, but from comparison with other
> >>>>>>> carcharodontosaurs, the following is hypothesized [*ibid*]:
> >>>>>>>
> >>>>>>> "The 26-foot-long (8 meters) beast weighed 2,200 pounds (1,000 kilograms), making it longer than an African elephant and heavier than a bison. Researchers named it *Ulughbegsaurus* *uzbekistanensis*, after Ulugh Beg, a 15th-century astronomer, mathematician and sultan from what is now Uzbekistan.
> >>>>>>>
> >>>>>>> "What caught scientists by surprise was that the dinosaur was much larger — twice the length and more than five times heavier — than its ecosystem's previously known apex predator: a tyrannosaur, the researchers found."
> >>>
> >>> If you look at the illustrations, you can see that it is a relatively small fragment of the upper jaw,
> >>> making me wonder how they got it so neatly into the phylogeny and thus were able
> >>> to extrapolate from known specimens.
> >>>
> >>> And I wonder how well they took into account the principle that as an organism evolves
> >>> to a much greater size, some parts of the anatomy increase more than others.
> >>> There were some pretty careless estimates made just from the sizes of various
> >>> teeth in homininae, and it might have actually come as a surprise to some paleontologists
> >>> to learn that *Gigantopithecus* really was the size one would expect from its huge molars.
> >>>
> >>>
> >>>
> >>>>> I'm pretty sure that the word the authors were looking for is "impacted."
> >>>> I think they mean "implanted", likely a new tooth that was yet to emerge
> >>>> from the jaw.
> >>>
> >>> Did you study the illustrations to see whether this is what they meant?
> >>>
> >>> By the way, do you have some grounds for thinking "implanted" is a synonym for "unerupted"?
> >
> >> It seems clear that's what they meant, as it was exposed only because of
> >> a break in the maxilla.
> >
> > You are evading the question. Are you afraid to say that the authors may have been guilty
> > of a malapropism?

<snip continuing evasion of question>

> >> I see you have located the actual paper,
> >> https://royalsocietypublishing.org/doi/10.1098/rsos.210923#d1e809
> >
> > I see you didn't notice that I included it in the OP. Did I make it too boring for you to read
> > it without getting sleepy?

> Don't see it here. Did someone snip it?

You can't see the OP? I can see it here in Google Groups. Looks like Giganews is letting you down.

> >>> Back to the specimen. On a thread about a Cambrian invertebrate [IIRC a stem arthropod]
> >>> you were disappointed by the lack of a phylogenetic analysis. The following should put you
> >>> in hog heaven where this "shark-tooth" is concerned:
> >>>
> >>> "Two phylogenetic analyses, each including the new taxon Ulughbegsaurus, were conducted with the
> >>> software TNT v. 1.5 [41] (electronic supplementary material, text S1: figures S3 and S4). Our first
> >>> analysis was performed using the data matrix proposed by Carrano et al. [42] then modified by
> >>> Hendrickx & Mateus [10] where Eoraptor represents the outgroup; the characters are treated as
> >>> unordered. Our second analysis was conducted using the matrix originally proposed by Porfiri et al.
> >>> [43] then modified by Chokchaloemwong et al. [40] where Ceratosaurus represents the outgroup;
> >>> characters 2, 4, 6, 13, 15, 17, 27, 69, 106, 148, 155, 158, 160, 167, 169, 171, 179, 181, 194, 195, 205, 208,
> >>> 217, 233, 241, 259, 267, 271 were treated as ordered. A traditional heuristic search was done with 1000
> >>> replicates of Wagner trees using random addition sequences, followed by the tree bisection and
> >>> reconnection branch swapping that holds 10 trees per replicate. Consistency index and retention index
> >>> were calculated with PAUP 4.0a [44]."
> >>> https://royalsocietypublishing.org/doi/pdf/10.1098/rsos.210923 [Section 4, paragraph 1]
> >>>
> >>> What does "were treated as ordered" mean?
> >
> >> A multistate character can be either ordered or unordered. If unordered,
> >> going from one state to any other takes one step. If ordered, going from
> >> state 1 to state 3 requires two steps, etc.
> >
> > Ah, like state 1 feathers (dinofuzz, optimistically called protofeathers), state 2 feathers,
> > state 3 feathers [barbs but no barbules, as in kiwis], state 4 feathers, and state 5 asymmetric flight remiges?

> That depends on how you choose to code them. What you have there is a
> multi-state character, but you have provided no information on whether
> it's to be considered ordered or unordered in analysis.

What, don't you remember Prum's hypothetical stages in the evolution of feathers?
You seemed to be quite a fan of his about half a dozen years ago.

> > But you don't include any of these in your phylogenetic analyses, despite a "consensus" that the majority of
> > coelurosaurs had at least state 1, eh?

> Yes. The consensus is based on the phylogenetic distribution of known
> feathers and optimization on a tree constructed from other data. The
> sparse data for feathers just don't contribute much to supporting a tree
> even if you include them.

So you think that, unlike the case of mammalian hair, loss of feathers in non-avian dinosaurs
was a great rarity?

> >>> The section continued with:
> >>>
> >>> "The first phylogenetic analysis produced 6320 most parsimonious treeswith a strict consensus tree placing
> >>> Ulughbegsaurus within a poorly resolved Neovenatoridae (Aerosteon, Australovenator, Chilantaisaurus,
> >>> Fukuiraptor, Megaraptor and Neovenator), a clade within Carcharodontosauria (figure 3a).
> >>>
> >>> How can there be so many "most parsimonous trees"? Is there a quantitative measure of parsimony,
> >>> or is it just an order ranking, with 6320 maximal trees, none of which is comparable to any of the others?
> >
> >> The quantitative measure is the number of steps (changes) required to
> >> fit the data to the tree. Not sure what you mean by "maximal" here;
> >
> > Not all orderings are linear. Take the proper subsets of the set {1, 2, 3} with the order "is a subset of";
> > by proper subset I mean a subset missing at least one element. The maximal proper subsets
> > are {1,2}, {2,3} and {1,3}. They are maximal, because there is no proper subset that contains any
> > of them without being that subset itself.

> This has nothing at all to do with the meaning of "most parsimonious
> trees". Nor does "maximal".

Thanks for clearing up that much. But it seems that biologists sometimes work with an
impoverished model where you try too hard to shoehorn things into linear order,
and even to assign numbers to them. [Mohs scale of hardness was a lot like that,
until some physics-savvy person fixed it up.]

On the other hand, in a phylogenetic tree, EVERY SPECIES is incomparable to every
other species. ALL species are at maximal points, at the tips of all the branches.
I could kick myself for not thinking of this example right off the bat.

> >> these are the trees that require the least number of steps. The trees
> >> are not identical, but only a few polytomies can produce a lot of trees.
> >> It seems that figure 3 shows strict consensus trees, i.e. the nodes that
> >> all the trees agree on. As you can see, there's plenty of agreement.

> >
> >>> "Neovenatoridae
> >>> was supported by 12 synapomorphies in this analysis, which includes two characters of the maxilla (i.e.
> >>> small foramen of promaxillary fenestra and sculptured external surface of maxilla and nasal). The second
> >>> phylogenetic analysis produced 284 most parsimonious trees with a strict consensus tree recovering
> >>> Ulughbegsaurus within Carcharodontosauria where Ulughbegsaurus, Siamraptor, Eocarcharia, Neovenator,
> >>> Concavenator and the clade of Acrocanthosaurus, Shaochilong and Carcharodontosaurinae all form a
> >>> polytomy (figure 3b).
> >>>
> >>> Wow, big time disagreement with other "consensus" tree. Are such things taken
> >>> in their stride by your favorite systematists?
> >
> >> Usually one attempts to determine the causes of conflict and resolve
> >> them. In this case the analyses use different characters, and somebody
> >> ought to look at that.

Did they give you enough information to combine the two sets of characters, and
to then see what happens?

> >> Of course only the maxillary characters are known
> >> for the focal taxon, so maybe they didn't feel like going to the trouble.

I've decided to make a fresh start on the paragraph on which we obviously
didn't connect. So I'll repost the paragraph later today, with my comments, but
without any distracting marginal attribution marks, and then we can try to communicate about it again.

Peter Nyikos
Professor, Dept. of Mathematics
Univ. of South Carolina -- standard disclaimer--
http://people.math.sc.edu/nyikos