On 9/14/22 6:53 AM, Popping Mad wrote:
>
>
>> Your ignorance of biology convinces you
>
>
> Your talking to the wrong guy. I studied biology for 4 years as part of
> the Pharmacy Degree and I am constantly up to date on the latest in
> Biological research

Perhaps, but you don't see up to date on phylogenetics. What journals
have you been reading?

Sorry to be so late with this, Ruben. I have been on a posting break which was originally slated
to end on Monday. By and large that is still the case, but I've found myself with a bit of
unexpected free time due to a previously scheduled activity being canceled.

I hope you are still reading this thread, because there are some very basic things
you need to know about the phylogeneitic trees by which John Harshman swears.

On Monday, September 12, 2022 at 9:04:51 PM UTC-4, Popping Mad wrote:
> On 9/12/22 11:23, John Harshman wrote:
> > Presumably. But my point is that you can't identify the internal nodes
> > with known species.
> and you can't assume they are edge nodes either. I am trying not to be a
> smart alleck or snooty here, but honestly, you really are failing to
> understand how silly this sounds.

Harshman is thoroughly committed to the reigning orthodoxy in systematics,
which dictates that ALL species be put at branch tips = end nodes.

[It also happens to use "nodes" exclusively for "internal nodes" -- hence your use
of "node" for what he calls "branch tips" is unintelligible to Harshman.]

The traditional evolutionary tree for Equioidea which Kathleen Hunt puts in her excellent
horse FAQ is anathema to Harshman:

http://www.talkorigins.org/faqs/horses/horse_evol.html

In fact, I'm surprised that Harshman hasn't tried to have that FAQ removed and
replaced by one of his liking. As far as he is concerned, the FAQ and especially
the tree is riddled with "lies" by his standards.

Harshman is so adamant about this that he even refuses to agree to the concept of
"prime ancestor candidate" as a designator of species/genera at internal nodes.
By this I mean a species/genus with an essentially complete known skeleton
(albeit distributed among several fossils in most cases) with NO characters
that would bar it from direct ancestry to the next taxon to which it is connected upwards.

> If all your known species are tips, your model is broken fundementally.

I don't know whether Harshman would agree to a compromise such as the following:
modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
the complete lack of disqualifying characters.

His usual comeback to such proposals is, "I don't see any use for such a thing."

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

On Wednesday, September 14, 2022 at 11:21:54 AM UTC-4, John Harshman wrote:
> On 9/14/22 6:53 AM, Popping Mad wrote:
> >
> >
> >> Your ignorance of biology convinces you

Ruben was merciful to you, John, by deleting your continuation:

"... that you know all the biology you need to know.
And you won't listen to a biologist. Why are you even here?"

This reminds me of a statement made by perhaps the greatest amateur
ichthyologist of all time, J. L. B. Smith, who made the living coelacanth
know to the scientific world with a superbly written article in a leading journal:

"Another type of intellectual snobbery is the dictum that science has now passed beyond the understanding of the ordinary man. That, however, is very largely a matter of presentation. With the possible exception of higher mathematics, there is not a single branch of science whose broad outlines the ordinary man cannot appreciate if it is properly explained to him.
--J.L.B. Smith, _The Search Beneath the Sea_, Henry Holt and Company, 1956, p. 44

> > Your talking to the wrong guy. I studied biology for 4 years as part of
> > the Pharmacy Degree and I am constantly up to date on the latest in
> > Biological research

> Perhaps, but you don't see up to date on phylogenetics. What journals
> have you been reading?

What sort of wild goose chase are you trying to send Ruben on? As far as this thread
is concerned, I told Ruben all he needs to know about phylogenetic trees a few minutes ago.

If you want to tell him how all the software used by you cladists puts every species
that is fed into it at the branch tips, you should be able to tell him yourself; he seems
to know enough about computer programming to understand if you can "properly explain"
how it goes to him.

Finally, if you want him to see the "reasoning" that puts all species at branch tips, you
should either give him a precise reference or try to explain it yourself. But I doubt that
he will impressed by your favorite terms, "objective" and "imaginary taxa" without
you justifying the ameliorative term and the pejorative term in ways to which you are unaccustomed.

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

On 9/22/22 4:02 AM, Peter Nyikos wrote:
> Sorry to be so late with this, Ruben. I have been on a posting break which was originally slated
> to end on Monday. By and large that is still the case, but I've found myself with a bit of
> unexpected free time due to a previously scheduled activity being canceled.
>
> I hope you are still reading this thread, because there are some very basic things
> you need to know about the phylogeneitic trees by which John Harshman swears.
>
>
> On Monday, September 12, 2022 at 9:04:51 PM UTC-4, Popping Mad wrote:
>> On 9/12/22 11:23, John Harshman wrote:
>>> Presumably. But my point is that you can't identify the internal nodes
>>> with known species.
>> and you can't assume they are edge nodes either. I am trying not to be a
>> smart alleck or snooty here, but honestly, you really are failing to
>> understand how silly this sounds.
>
> Harshman is thoroughly committed to the reigning orthodoxy in systematics,
> which dictates that ALL species be put at branch tips = end nodes.
>
> [It also happens to use "nodes" exclusively for "internal nodes" -- hence your use
> of "node" for what he calls "branch tips" is unintelligible to Harshman.]

You aren't reading. The term is "terminal node", as opposed to "internal
node".

> The traditional evolutionary tree for Equioidea which Kathleen Hunt puts in her excellent
> horse FAQ is anathema to Harshman:
>
> http://www.talkorigins.org/faqs/horses/horse_evol.html
>
> In fact, I'm surprised that Harshman hasn't tried to have that FAQ removed and
> replaced by one of his liking. As far as he is concerned, the FAQ and especially
> the tree is riddled with "lies" by his standards.
>
> Harshman is so adamant about this that he even refuses to agree to the concept of
> "prime ancestor candidate" as a designator of species/genera at internal nodes.
> By this I mean a species/genus with an essentially complete known skeleton
> (albeit distributed among several fossils in most cases) with NO characters
> that would bar it from direct ancestry to the next taxon to which it is connected upwards.
>
>
>> If all your known species are tips, your model is broken fundementally.
>
> I don't know whether Harshman would agree to a compromise such as the following:
> modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
> are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
> the complete lack of disqualifying characters.

This would be the natural result of any usual phylogenetic analysis of
such taxa. No special procedure necessary, as long as a taxon had zero
autapomorphies.

> His usual comeback to such proposals is, "I don't see any use for such a thing."

And you have never been able to explain a use.

On Thursday, September 22, 2022 at 9:27:42 AM UTC-4, John Harshman wrote:
> On 9/22/22 4:02 AM, Peter Nyikos wrote:
> > Sorry to be so late with this, Ruben. I have been on a posting break which was originally slated
> > to end on Monday. By and large that is still the case, but I've found myself with a bit of
> > unexpected free time due to a previously scheduled activity being canceled.

Now a tiny window has opened between successive activities, just long enough
to post this and maybe another short post.

> >
> > I hope you are still reading this thread, because there are some very basic things
> > you need to know about the phylogeneitic trees by which John Harshman swears.

> >
> > On Monday, September 12, 2022 at 9:04:51 PM UTC-4, Popping Mad wrote:
> >> On 9/12/22 11:23, John Harshman wrote:
> >>> Presumably. But my point is that you can't identify the internal nodes
> >>> with known species.
> >> and you can't assume they are edge nodes either. I am trying not to be a
> >> smart alleck or snooty here, but honestly, you really are failing to
> >> understand how silly this sounds.
> >
> > Harshman is thoroughly committed to the reigning orthodoxy in systematics,
> > which dictates that ALL species be put at branch tips = end nodes.
> >
> > [It also happens to use "nodes" exclusively for "internal nodes" -- hence your use
> > of "node" for what he calls "branch tips" is unintelligible to Harshman..]

> You aren't reading. The term is "terminal node", as opposed to "internal
> node".

I have been reading Gould, inter alia:

"The extreme rarity of transitional forms in the fossil record persist as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils."
--Stephen J. Gould - "Evolution's Erratic Pace," _Natural History_,vol. 86(5) (May 1987): pp. 12-16, at p. 14 Reprinted in _The Panda's Thumb_, pp. 181-182.

Note, tips AND nodes. Granted, this was before the orthodoxy started to reign
in earnest on the following year, with the final victory in the cladist wars.

But make no mistake: when Gould wrote the above,
he was writing about "evolutionary trees" and NOT "phylogenetic trees".
IOW, he was writing about trees like that of Kathleen Hunt:

> > The traditional evolutionary tree for Equioidea which Kathleen Hunt puts in her excellent
> > horse FAQ is anathema to Harshman:
> >
> > http://www.talkorigins.org/faqs/horses/horse_evol.html
> >
> > In fact, I'm surprised that Harshman hasn't tried to have that FAQ removed and
> > replaced by one of his liking. As far as he is concerned, the FAQ and especially
> > the tree is riddled with "lies" by his standards.

Do you deny that you have used "lies" and "lying" for exactly what Kathleen Hunt is doing
numerous times in the FAQ and at all but the branch tips in her *evolutionary* tree?

> > Harshman is so adamant about this that he even refuses to agree to the concept of
> > "prime ancestor candidate" as a designator of species/genera at internal nodes.
> > By this I mean a species/genus with an essentially complete known skeleton
> > (albeit distributed among several fossils in most cases) with NO characters
> > that would bar it from direct ancestry to the next taxon to which it is connected upwards.
> >
> >
> >> If all your known species are tips, your model is broken fundementally..
> >
> > I don't know whether Harshman would agree to a compromise such as the following:
> > modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
> > are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
> > the complete lack of disqualifying characters.

> This would be the natural result of any usual phylogenetic analysis of
> such taxa.

Oh, really? including the part about "thorns" as opposed to longish branches?

Or were you referring to trees at all? or only to the character analysis which
almost never specifies the number of apomorphies?

>No special procedure necessary, as long as a taxon had zero
> autapomorphies.

Why "autapomorphies"? phylogenetic trees use the legal fiction ("lie"?) that
every internal node has at least two branches emanating from it; so it would
be labeling the results of a fictitious cladogenesis.

> > His usual comeback to such proposals is, "I don't see any use for such a thing."

> And you have never been able to explain a use.

There were plenty of careful explanations, and you never had a good comeback besides
paraphrases of the broken record routine that I've quoted just now.

But I will be glad to repeat them if I know that an interested, knowledgeable
party is paying attention, like Ruben.

Btw I never made the "thorn tree" proposal before, so this last retort of yours is misleading.

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

On Thursday, September 22, 2022 at 9:36:27 AM UTC-7, peter2...@gmail.com wrote:
> On Thursday, September 22, 2022 at 9:27:42 AM UTC-4, John Harshman wrote:
> > On 9/22/22 4:02 AM, Peter Nyikos wrote:
> > > Sorry to be so late with this, Ruben. I have been on a posting break which was originally slated
> > > to end on Monday. By and large that is still the case, but I've found myself with a bit of
> > > unexpected free time due to a previously scheduled activity being canceled.
> Now a tiny window has opened between successive activities, just long enough
> to post this and maybe another short post.
> > >
> > > I hope you are still reading this thread, because there are some very basic things
> > > you need to know about the phylogeneitic trees by which John Harshman swears.
>
> > >
> > > On Monday, September 12, 2022 at 9:04:51 PM UTC-4, Popping Mad wrote:
> > >> On 9/12/22 11:23, John Harshman wrote:
> > >>> Presumably. But my point is that you can't identify the internal nodes
> > >>> with known species.
> > >> and you can't assume they are edge nodes either. I am trying not to be a
> > >> smart alleck or snooty here, but honestly, you really are failing to
> > >> understand how silly this sounds.
> > >
> > > Harshman is thoroughly committed to the reigning orthodoxy in systematics,
> > > which dictates that ALL species be put at branch tips = end nodes.
> > >
> > > [It also happens to use "nodes" exclusively for "internal nodes" -- hence your use
> > > of "node" for what he calls "branch tips" is unintelligible to Harshman.]
>
> > You aren't reading. The term is "terminal node", as opposed to "internal
> > node".
> I have been reading Gould, inter alia:
>
> "The extreme rarity of transitional forms in the fossil record persist as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils."
> --Stephen J. Gould - "Evolution's Erratic Pace," _Natural History_,vol. 86(5) (May 1987): pp. 12-16, at p. 14 Reprinted in _The Panda's Thumb_, pp. 181-182.
>
> Note, tips AND nodes. Granted, this was before the orthodoxy started to reign
> in earnest on the following year, with the final victory in the cladist wars.
>
> But make no mistake: when Gould wrote the above,
> he was writing about "evolutionary trees" and NOT "phylogenetic trees".
> IOW, he was writing about trees like that of Kathleen Hunt:
> > > The traditional evolutionary tree for Equioidea which Kathleen Hunt puts in her excellent
> > > horse FAQ is anathema to Harshman:
> > >
> > > http://www.talkorigins.org/faqs/horses/horse_evol.html
> > >
> > > In fact, I'm surprised that Harshman hasn't tried to have that FAQ removed and
> > > replaced by one of his liking. As far as he is concerned, the FAQ and especially
> > > the tree is riddled with "lies" by his standards.
> Do you deny that you have used "lies" and "lying" for exactly what Kathleen Hunt is doing
> numerous times in the FAQ and at all but the branch tips in her *evolutionary* tree?
> > > Harshman is so adamant about this that he even refuses to agree to the concept of
> > > "prime ancestor candidate" as a designator of species/genera at internal nodes.
> > > By this I mean a species/genus with an essentially complete known skeleton
> > > (albeit distributed among several fossils in most cases) with NO characters
> > > that would bar it from direct ancestry to the next taxon to which it is connected upwards.
> > >
Interesting, a complete skeleton of a species or genus, with no characters that would allow anything but direct ancestry to the next species that evolved from it. Just so you know, just-so.
> > >
> > >> If all your known species are tips, your model is broken fundementally.
> > >
> > > I don't know whether Harshman would agree to a compromise such as the following:
> > > modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
> > > are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
> > > the complete lack of disqualifying characters.
>
> > This would be the natural result of any usual phylogenetic analysis of
> > such taxa.
> Oh, really? including the part about "thorns" as opposed to longish branches?
>
> Or were you referring to trees at all? or only to the character analysis which
> almost never specifies the number of apomorphies?
> >No special procedure necessary, as long as a taxon had zero
> > autapomorphies.
> Why "autapomorphies"? phylogenetic trees use the legal fiction ("lie"?) that
> every internal node has at least two branches emanating from it; so it would
> be labeling the results of a fictitious cladogenesis.
> > > His usual comeback to such proposals is, "I don't see any use for such a thing."
>
> > And you have never been able to explain a use.
> There were plenty of careful explanations, and you never had a good comeback besides
> paraphrases of the broken record routine that I've quoted just now.
>
> But I will be glad to repeat them if I know that an interested, knowledgeable
> party is paying attention, like Ruben.
>
> Btw I never made the "thorn tree" proposal before, so this last retort of yours is misleading.
>
>
> Peter Nyikos
> Professor, Dept. of Mathematics -- standard disclaimer--
> Univ. of So. Carolina in Columbia
> http://people.math.sc.edu/nyikos

On 9/22/22 9:36 AM, Peter Nyikos wrote:
> On Thursday, September 22, 2022 at 9:27:42 AM UTC-4, John Harshman wrote:
>> On 9/22/22 4:02 AM, Peter Nyikos wrote:
>>> Sorry to be so late with this, Ruben. I have been on a posting break which was originally slated
>>> to end on Monday. By and large that is still the case, but I've found myself with a bit of
>>> unexpected free time due to a previously scheduled activity being canceled.
>
> Now a tiny window has opened between successive activities, just long enough
> to post this and maybe another short post.
>
>>>
>>> I hope you are still reading this thread, because there are some very basic things
>>> you need to know about the phylogeneitic trees by which John Harshman swears.
>
>>>
>>> On Monday, September 12, 2022 at 9:04:51 PM UTC-4, Popping Mad wrote:
>>>> On 9/12/22 11:23, John Harshman wrote:
>>>>> Presumably. But my point is that you can't identify the internal nodes
>>>>> with known species.
>>>> and you can't assume they are edge nodes either. I am trying not to be a
>>>> smart alleck or snooty here, but honestly, you really are failing to
>>>> understand how silly this sounds.
>>>
>>> Harshman is thoroughly committed to the reigning orthodoxy in systematics,
>>> which dictates that ALL species be put at branch tips = end nodes.
>>>
>>> [It also happens to use "nodes" exclusively for "internal nodes" -- hence your use
>>> of "node" for what he calls "branch tips" is unintelligible to Harshman.]
>
>> You aren't reading. The term is "terminal node", as opposed to "internal
>> node".
>
> I have been reading Gould, inter alia:
>
> "The extreme rarity of transitional forms in the fossil record persist as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils."
> --Stephen J. Gould - "Evolution's Erratic Pace," _Natural History_,vol. 86(5) (May 1987): pp. 12-16, at p. 14 Reprinted in _The Panda's Thumb_, pp. 181-182.
>
> Note, tips AND nodes. Granted, this was before the orthodoxy started to reign
> in earnest on the following year, with the final victory in the cladist wars.

Gould was writing for a lay audience and wasn't a systematist in any
case. He probably wasn't up on the language used in phylogenetics. On
the other hand, I am.

> But make no mistake: when Gould wrote the above,
> he was writing about "evolutionary trees" and NOT "phylogenetic trees".
> IOW, he was writing about trees like that of Kathleen Hunt:

Yes, that seems to be true. When he says "node" above, he does seem to
mean "internal node". What is the relevance?

>>> The traditional evolutionary tree for Equioidea which Kathleen Hunt puts in her excellent
>>> horse FAQ is anathema to Harshman:
>>>
>>> http://www.talkorigins.org/faqs/horses/horse_evol.html
>>>
>>> In fact, I'm surprised that Harshman hasn't tried to have that FAQ removed and
>>> replaced by one of his liking. As far as he is concerned, the FAQ and especially
>>> the tree is riddled with "lies" by his standards.
>
> Do you deny that you have used "lies" and "lying" for exactly what Kathleen Hunt is doing
> numerous times in the FAQ and at all but the branch tips in her *evolutionary* tree?

I don't deny. Why do you ask?

>>> Harshman is so adamant about this that he even refuses to agree to the concept of
>>> "prime ancestor candidate" as a designator of species/genera at internal nodes.
>>> By this I mean a species/genus with an essentially complete known skeleton
>>> (albeit distributed among several fossils in most cases) with NO characters
>>> that would bar it from direct ancestry to the next taxon to which it is connected upwards.
>>>
>>>
>>>> If all your known species are tips, your model is broken fundementally.
>>>
>>> I don't know whether Harshman would agree to a compromise such as the following:
>>> modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
>>> are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
>>> the complete lack of disqualifying characters.
>
>> This would be the natural result of any usual phylogenetic analysis of
>> such taxa.
>
> Oh, really? including the part about "thorns" as opposed to longish branches?

Yes, really. Do you understand what branch lengths represent?

> Or were you referring to trees at all? or only to the character analysis which
> almost never specifies the number of apomorphies?

No idea what you mean by that.

> >No special procedure necessary, as long as a taxon had zero
>> autapomorphies.
>
> Why "autapomorphies"? phylogenetic trees use the legal fiction ("lie"?) that
> every internal node has at least two branches emanating from it; so it would
> be labeling the results of a fictitious cladogenesis.

What you're trying to say there is also far from clear. A zero-length
branch is quite possible. If not that, what are you referring to?

>>> His usual comeback to such proposals is, "I don't see any use for such a thing."
>
>> And you have never been able to explain a use.
>
> There were plenty of careful explanations, and you never had a good comeback besides
> paraphrases of the broken record routine that I've quoted just now.

So you claim now. But you have a highly selective memory.

> But I will be glad to repeat them if I know that an interested, knowledgeable
> party is paying attention, like Ruben.
>
> Btw I never made the "thorn tree" proposal before, so this last retort of yours is misleading.

I thought you were talking about "ancestor candidates".

On Thursday, September 22, 2022 at 3:27:02 PM UTC-4, John Harshman wrote:
> On 9/22/22 9:36 AM, Peter Nyikos wrote:
> > On Thursday, September 22, 2022 at 9:27:42 AM UTC-4, John Harshman wrote:
> >> On 9/22/22 4:02 AM, Peter Nyikos wrote:
> >>> Sorry to be so late with this, Ruben. I have been on a posting break which was originally slated
> >>> to end on Monday. By and large that is still the case, but I've found myself with a bit of
> >>> unexpected free time due to a previously scheduled activity being canceled.
> >
> > Now a tiny window has opened between successive activities, just long enough
> > to post this and maybe another short post.
> >
> >>>
> >>> I hope you are still reading this thread, because there are some very basic things
> >>> you need to know about the phylogeneitic trees by which John Harshman swears.
> >
> >>>
> >>> On Monday, September 12, 2022 at 9:04:51 PM UTC-4, Popping Mad wrote:
> >>>> On 9/12/22 11:23, John Harshman wrote:
> >>>>> Presumably. But my point is that you can't identify the internal nodes
> >>>>> with known species.
> >>>> and you can't assume they are edge nodes either. I am trying not to be a
> >>>> smart alleck or snooty here, but honestly, you really are failing to
> >>>> understand how silly this sounds.
> >>>
> >>> Harshman is thoroughly committed to the reigning orthodoxy in systematics,
> >>> which dictates that ALL species be put at branch tips = end nodes.
> >>>
> >>> [It also happens to use "nodes" exclusively for "internal nodes" -- hence your use
> >>> of "node" for what he calls "branch tips" is unintelligible to Harshman.]
> >
> >> You aren't reading. The term is "terminal node", as opposed to "internal
> >> node".
> >
> > I have been reading Gould, inter alia:
> >
> > "The extreme rarity of transitional forms in the fossil record persist as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils."
> > --Stephen J. Gould - "Evolution's Erratic Pace," _Natural History_,vol. 86(5) (May 1987): pp. 12-16, at p. 14 Reprinted in _The Panda's Thumb_, pp.. 181-182.
> >
> > Note, tips AND nodes. Granted, this was before the orthodoxy started to reign
> > in earnest on the following year, with the final victory in the cladist wars.

> Gould was writing for a lay audience and wasn't a systematist in any
> case.

However, he was a biological polymath with a keen mind.

>He probably wasn't up on the language used in phylogenetics. On
> the other hand, I am.

Your use of "branch lengths" below suggests otherwise.

<snip for focus>

> >>> I don't know whether Harshman would agree to a compromise such as the following:
> >>> modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
> >>> are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
> >>> the complete lack of disqualifying characters.
> >
> >> This would be the natural result of any usual phylogenetic analysis of
> >> such taxa.
> >
> > Oh, really? including the part about "thorns" as opposed to longish branches?

> Yes, really. Do you understand what branch lengths represent?

Are you sure you know what you are talking about? In ALL the detailed
trees that we've talked about this year, branch lengths in the LITERAL
sense have to do with time elapsed. NONE of the numbers labeling
segments of those branches has anything to do with numbers
of apomorphies. Most numerical labels have to do with bootstrap values, and in
the last case below they give mya to the nearest 100,000 years.

Here they are:

fig. 5 in:
https://www.nature.com/articles/s41598-022-15535-6
branch lengths are governed by time-calibration based on stratigraphic record
[in epochs, not mya]

fig. 18 in paper coauthored by Mickey Mortimer:
https://peerj.com/articles/7247/?td=bl&fbclid=IwAR09VFddJNY8v0rvmEh9HmtINsJLScQj0B98UsoKEbTjMMNZLTdxZyA4h4w#systematic

Fig. 1 in https://academic.oup.com/gbe/article/9/9/2308/4095375
works as described, except that there is no explicit scale at top or bottom

With calibration explicitly at the top, in epochs AND mya:
Fig 1 in: https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals Fig. 1

Finally, the following was calibrated by mya at bottom and also division of periods into 2-3 sub-periods. But it also labeled every node by mya to the nearest tenth:
https://www.science.org/doi/10.1126/sciadv.abq1898

This last example was criticized by me for the way the authors didn't
expand the scale in the "G" part of the Permian. You ignored the author-elephants
in the room while exonerating the editors and reviewers:
https://groups.google.com/g/sci.bio.paleontology/c/26BZZ4NIrHw/m/LFjneBO9EgAJ

> > Or were you referring to trees at all? or only to the character analysis which
> > almost never specifies the number of apomorphies?
> No idea what you mean by that.

Perhaps the five examples will serve as a wake-up call to reorient
you as to what I was talking about. Perhaps my response
to a mostly useless question by you below could also serve this purpose.

> > >No special procedure necessary, as long as a taxon had zero
> >> autapomorphies.
> >
> > Why "autapomorphies"? phylogenetic trees use the legal fiction ("lie"?) that
> > every internal node has at least two branches emanating from it; so it would
> > be labeling the results of a fictitious cladogenesis.

> What you're trying to say there is also far from clear.

As usual, your question in response, below, is not designed to produce clarity.
You completely ignore the "fictitious cladogenesis" issue, and the
resulting problematic use of "autapomorphies" instead of the simple "apomorphies."

> A zero-length
> branch is quite possible. If not that, what are you referring to?

Zero-length branches are literally impossible [1] so you would have
to be referring to labeling, but there was no labeling of apomorphy numbers
in any of the five trees. [This is why I asked, "were you referring to trees at all?"]

[1] given that you are adamantly opposed to internal nodes being assigned
to known genera or species.

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

PS I will respond to the text I snipped for focus later,
and to the part I snipped at the end without marking the snip.

On 9/27/22 5:25 PM, Peter Nyikos wrote:
> On Thursday, September 22, 2022 at 3:27:02 PM UTC-4, John Harshman wrote:
>> On 9/22/22 9:36 AM, Peter Nyikos wrote:
>>> On Thursday, September 22, 2022 at 9:27:42 AM UTC-4, John Harshman wrote:
>>>> On 9/22/22 4:02 AM, Peter Nyikos wrote:
>>>>> Sorry to be so late with this, Ruben. I have been on a posting break which was originally slated
>>>>> to end on Monday. By and large that is still the case, but I've found myself with a bit of
>>>>> unexpected free time due to a previously scheduled activity being canceled.
>>>
>>> Now a tiny window has opened between successive activities, just long enough
>>> to post this and maybe another short post.
>>>
>>>>>
>>>>> I hope you are still reading this thread, because there are some very basic things
>>>>> you need to know about the phylogeneitic trees by which John Harshman swears.
>>>
>>>>>
>>>>> On Monday, September 12, 2022 at 9:04:51 PM UTC-4, Popping Mad wrote:
>>>>>> On 9/12/22 11:23, John Harshman wrote:
>>>>>>> Presumably. But my point is that you can't identify the internal nodes
>>>>>>> with known species.
>>>>>> and you can't assume they are edge nodes either. I am trying not to be a
>>>>>> smart alleck or snooty here, but honestly, you really are failing to
>>>>>> understand how silly this sounds.
>>>>>
>>>>> Harshman is thoroughly committed to the reigning orthodoxy in systematics,
>>>>> which dictates that ALL species be put at branch tips = end nodes.
>>>>>
>>>>> [It also happens to use "nodes" exclusively for "internal nodes" -- hence your use
>>>>> of "node" for what he calls "branch tips" is unintelligible to Harshman.]
>>>
>>>> You aren't reading. The term is "terminal node", as opposed to "internal
>>>> node".
>>>
>>> I have been reading Gould, inter alia:
>>>
>>> "The extreme rarity of transitional forms in the fossil record persist as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils."
>>> --Stephen J. Gould - "Evolution's Erratic Pace," _Natural History_,vol. 86(5) (May 1987): pp. 12-16, at p. 14 Reprinted in _The Panda's Thumb_, pp. 181-182.
>>>
>>> Note, tips AND nodes. Granted, this was before the orthodoxy started to reign
>>> in earnest on the following year, with the final victory in the cladist wars.
>
>> Gould was writing for a lay audience and wasn't a systematist in any
>> case.
>
> However, he was a biological polymath with a keen mind.

True, but he wasn't that up on phylogenetic methods.

>> He probably wasn't up on the language used in phylogenetics. On
>> the other hand, I am.
>
> Your use of "branch lengths" below suggests otherwise.

Not understanding what you mean by that. Are you saying that "branch
length" isn't a term used in phylogenetics?

>>>>> I don't know whether Harshman would agree to a compromise such as the following:
>>>>> modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
>>>>> are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
>>>>> the complete lack of disqualifying characters.
>>>
>>>> This would be the natural result of any usual phylogenetic analysis of
>>>> such taxa.
>>>
>>> Oh, really? including the part about "thorns" as opposed to longish branches?
>
>> Yes, really. Do you understand what branch lengths represent?
>
> Are you sure you know what you are talking about? In ALL the detailed
> trees that we've talked about this year, branch lengths in the LITERAL
> sense have to do with time elapsed. NONE of the numbers labeling
> segments of those branches has anything to do with numbers
> of apomorphies. Most numerical labels have to do with bootstrap values, and in
> the last case below they give mya to the nearest 100,000 years.

This is sometimes the case. Branch lengths can be scaled to number of
changes, to time, or to nothing at all. But in the case we were talking
about, it's the former. Would you like to see examples of such trees?
They're pretty common. Further, even when branch lengths aren't
displayed in a figure, the analysis used to construct the figure does
come up with branch lengths that represent the number of changes.

> Here they are:
>
> fig. 5 in:
> https://www.nature.com/articles/s41598-022-15535-6
> branch lengths are governed by time-calibration based on stratigraphic record
> [in epochs, not mya]

Correct.

> fig. 18 in paper coauthored by Mickey Mortimer:
> https://peerj.com/articles/7247/?td=bl&fbclid=IwAR09VFddJNY8v0rvmEh9HmtINsJLScQj0B98UsoKEbTjMMNZLTdxZyA4h4w#systematic

Note that in Fig. 17 the branch lengths mean nothing.

> Fig. 1 in https://academic.oup.com/gbe/article/9/9/2308/4095375
> works as described, except that there is no explicit scale at top or bottom

Not sure what "as described" means, but the branches in that tree are
scaled by number of changes, if that's what you mean. (Incidentally,
that's sometimes called a phylogram to distinguish from an unscaled
cladogram.)

> With calibration explicitly at the top, in epochs AND mya:
> Fig 1 in: https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals Fig. 1

That link goes only to the abstract and, for some reason, Fig. 3. So I
don't know.

> Finally, the following was calibrated by mya at bottom and also division of periods into 2-3 sub-periods. But it also labeled every node by mya to the nearest tenth:
> https://www.science.org/doi/10.1126/sciadv.abq1898

Correct.

> This last example was criticized by me for the way the authors didn't
> expand the scale in the "G" part of the Permian. You ignored the author-elephants
> in the room while exonerating the editors and reviewers:
> https://groups.google.com/g/sci.bio.paleontology/c/26BZZ4NIrHw/m/LFjneBO9EgAJ

You never forget a grudge.

>>> Or were you referring to trees at all? or only to the character analysis which
>>> almost never specifies the number of apomorphies?
>> No idea what you mean by that.
>
> Perhaps the five examples will serve as a wake-up call to reorient
> you as to what I was talking about. Perhaps my response
> to a mostly useless question by you below could also serve this purpose.

Your sample of trees is highly biased. It's true that fossil-based trees
very commonly show branch lengths scaled to time, and many trees show
branch length scaled to nothing. But molecular trees commonly show
branch lengths scaled to number of changes, as in the one molecular
study you mention above. More importantly, such a tree is what I was
talking about, and it would show your "thorns" automatically.

>>>> No special procedure necessary, as long as a taxon had zero
>>>> autapomorphies.
>>>
>>> Why "autapomorphies"? phylogenetic trees use the legal fiction ("lie"?) that
>>> every internal node has at least two branches emanating from it; so it would
>>> be labeling the results of a fictitious cladogenesis.
>
>> What you're trying to say there is also far from clear.
>
> As usual, your question in response, below, is not designed to produce clarity.
> You completely ignore the "fictitious cladogenesis" issue, and the
> resulting problematic use of "autapomorphies" instead of the simple "apomorphies."

I don't know what the fictitious cladogenesis issue is. Nor do I
understand why autapomorphies would be the wrong word. Do you see, by
the way, how you constantly accuse me of dishonesty? That's not a good
way to have a discussion.

>> A zero-length
>> branch is quite possible. If not that, what are you referring to?
>
> Zero-length branches are literally impossible [1] so you would have
> to be referring to labeling, but there was no labeling of apomorphy numbers
> in any of the five trees. [This is why I asked, "were you referring to trees at all?"]

Autapomorphy numbers would be shown as the terminal branch lengths of
any tree scaled to number of changes. A branch with a length of zero
would not stick out from the ancestral node. I could point you to a few
real examples if you liked; they can occur on trees built from small
data sets.

On Tuesday, September 27, 2022 at 9:16:05 PM UTC-4, John Harshman wrote:
> On 9/27/22 5:25 PM, Peter Nyikos wrote:
> > On Thursday, September 22, 2022 at 3:27:02 PM UTC-4, John Harshman wrote:
> >> On 9/22/22 9:36 AM, Peter Nyikos wrote:
> >>> On Thursday, September 22, 2022 at 9:27:42 AM UTC-4, John Harshman wrote:
> >>>> On 9/22/22 4:02 AM, Peter Nyikos wrote:

[to Ruben, aka Popping mad:]
> >>>>> I hope you are still reading this thread, because there are some very basic things
> >>>>> you need to know about the phylogeneitic trees by which John Harshman swears.
> >>>
> >>>>>
> >>>>> On Monday, September 12, 2022 at 9:04:51 PM UTC-4, Popping Mad wrote:
> >>>>>> On 9/12/22 11:23, John Harshman wrote:
> >>>>>>> Presumably. But my point is that you can't identify the internal nodes
> >>>>>>> with known species.
> >>>>>> and you can't assume they are edge nodes either. I am trying not to be a
> >>>>>> smart alleck or snooty here, but honestly, you really are failing to
> >>>>>> understand how silly this sounds.

Unfortunately, Ruben seems to have gone incommunicado for an indefinite
period of time, and he may never see the following explanation:

> >>>>> Harshman is thoroughly committed to the reigning orthodoxy in systematics,
> >>>>> which dictates that ALL species be put at branch tips = end nodes..
> >>>>>
> >>>>> [It also happens to use "nodes" exclusively for "internal nodes" -- hence your use
> >>>>> of "node" for what he calls "branch tips" is unintelligible to Harshman.]
> >>>
> >>>> You aren't reading. The term is "terminal node", as opposed to "internal
> >>>> node".
> >>>
> >>> I have been reading Gould, inter alia:
> >>>
> >>> "The extreme rarity of transitional forms in the fossil record persist as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils."
> >>> --Stephen J. Gould - "Evolution's Erratic Pace," _Natural History_,vol. 86(5) (May 1987): pp. 12-16, at p. 14 Reprinted in _The Panda's Thumb_, pp. 181-182.
> >>>
> >>> Note, tips AND nodes. Granted, this was before the orthodoxy started to reign
> >>> in earnest on the following year, with the final victory in the cladist wars.
> >
> >> Gould was writing for a lay audience and wasn't a systematist in any
> >> case.
> >
> > However, he was a biological polymath with a keen mind.

> True, but he wasn't that up on phylogenetic methods.

Methods of constructing phylogenetic trees are irrelevant
to the issue at hand, which is that these trees are designed to implicitly
deny direct ancestry to every single pair of taxa since the beginning of life on earth.

> >> He probably wasn't up on the language used in phylogenetics. On
> >> the other hand, I am.
> >
> > Your use of "branch lengths" below suggests otherwise.

> Not understanding what you mean by that. Are you saying that "branch
> length" isn't a term used in phylogenetics?

If you had understood what I wrote directly above, and below, instead of shooting
from the hip, you wouldn't have asked this asinine question.

> >>>>> I don't know whether Harshman would agree to a compromise such as the following:
> >>>>> modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
> >>>>> are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
> >>>>> the complete lack of disqualifying characters.
> >>>
> >>>> This would be the natural result of any usual phylogenetic analysis of
> >>>> such taxa.
> >>>
> >>> Oh, really? including the part about "thorns" as opposed to longish branches?

It turns out, far below, that "usual" means "molecular" and is useless for
the kind of project I envision above.

> >> Yes, really. Do you understand what branch lengths represent?

> > Are you sure you know what you are talking about? In ALL the detailed
> > trees that we've talked about this year, branch lengths in the LITERAL
> > sense have to do with time elapsed. NONE of the numbers labeling
> > segments of those branches has anything to do with numbers
> > of apomorphies. Most numerical labels have to do with bootstrap values, and in
> > the last case below they give mya to the nearest 100,000 years.

> This is sometimes the case.

"sometimes" seems to be a huge understatement.

> Branch lengths can be scaled to number of
> changes, to time, or to nothing at all. But in the case we were talking
> about, it's the former. Would you like to see examples of such trees?

You are shooting from the hip again without reading further.
You gave one below [keyword: phylogram]. Unfortunately,
none of the branch lengths is anywhere near 0, so it doesn't
really answer my question.

Besides, what kept you from producing SEVERAL one reply earlier?
Why do you want to drag the discussion out, unlike me, who provided FIVE
examples *immediately*?

> They're pretty common. Further, even when branch lengths aren't
> displayed in a figure, the analysis used to construct the figure does
> come up with branch lengths that represent the number of changes.

Finally, you are using "branch lengths" literally. But I'd still love to SEE
(as opposed to being told by you that it has been done)
how they manage a branch length that represents 0 apomorphies.

> > Here they are:
> >
> > fig. 5 in:
> > https://www.nature.com/articles/s41598-022-15535-6
> > branch lengths are governed by time-calibration based on stratigraphic record
> > [in epochs, not mya]

> Correct.

> > fig. 18 in paper coauthored by Mickey Mortimer:
> > https://peerj.com/articles/7247/?td=bl&fbclid=IwAR09VFddJNY8v0rvmEh9HmtINsJLScQj0B98UsoKEbTjMMNZLTdxZyA4h4w#systematic
> Note that in Fig. 17 the branch lengths mean nothing.

That's why I didn't talk about Fig. 17. Duh.

> > Fig. 1 in https://academic.oup.com/gbe/article/9/9/2308/4095375
> > works as described, except that there is no explicit scale at top or bottom
> Not sure what "as described" means, but the branches in that tree are
> scaled by number of changes, if that's what you mean. (Incidentally,
> that's sometimes called a phylogram to distinguish from an unscaled
> cladogram.)

Correct, now that I am looking more closely. But the shortest branch lengths
go to Homo sapiens vis a vis Pan paniscus, and to the walrus vis a vis sea lions.
So we are very far from a "thorn tree".

> > With calibration explicitly at the top, in epochs AND mya:
> > Fig 1 in: https://www.researchgate.net/publication/235423191_The_Placental_Mammal_Ancestor_and_the_Post-K-Pg_Radiation_of_Placentals Fig. 1
> That link goes only to the abstract and, for some reason, Fig. 3. So I
> don't know.

Didn't you get two icons labeled "Download full-length PDF" and "Read full-text" in the upper right corner?

> > Finally, the following was calibrated by mya at bottom and also division of periods into 2-3 sub-periods. But it also labeled every node by mya to the nearest tenth:
> > https://www.science.org/doi/10.1126/sciadv.abq1898
> Correct.
> > This last example was criticized by me for the way the authors didn't
> > expand the scale in the "G" part of the Permian. You ignored the author-elephants
> > in the room while exonerating the editors and reviewers:
> > https://groups.google.com/g/sci.bio.paleontology/c/26BZZ4NIrHw/m/LFjneBO9EgAJ

> You never forget a grudge.

Here grudge = first time mention of something that happened less than a week ago.

You keep coming across as someone with a childish belief in the magic of words
(grudge, traitor, megalomania, paranoid, etc.) whose usage you stretch well past the breaking point.

> >>> Or were you referring to trees at all? or only to the character analysis which
> >>> almost never specifies the number of apomorphies?
> >> No idea what you mean by that.
> >
> > Perhaps the five examples will serve as a wake-up call to reorient
> > you as to what I was talking about. Perhaps my response
> > to a mostly useless question by you below could also serve this purpose..

On 9/30/22 7:57 AM, Peter Nyikos wrote:
> On Tuesday, September 27, 2022 at 9:16:05 PM UTC-4, John Harshman wrote:
>> On 9/27/22 5:25 PM, Peter Nyikos wrote:
>>> On Thursday, September 22, 2022 at 3:27:02 PM UTC-4, John Harshman wrote:
>>>> On 9/22/22 9:36 AM, Peter Nyikos wrote:
>>>>> On Thursday, September 22, 2022 at 9:27:42 AM UTC-4, John Harshman wrote:
>>>>>> On 9/22/22 4:02 AM, Peter Nyikos wrote:
>
> [to Ruben, aka Popping mad:]
>>>>>>> I hope you are still reading this thread, because there are some very basic things
>>>>>>> you need to know about the phylogeneitic trees by which John Harshman swears.
>>>>>
>>>>>>>
>>>>>>> On Monday, September 12, 2022 at 9:04:51 PM UTC-4, Popping Mad wrote:
>>>>>>>> On 9/12/22 11:23, John Harshman wrote:
>>>>>>>>> Presumably. But my point is that you can't identify the internal nodes
>>>>>>>>> with known species.
>>>>>>>> and you can't assume they are edge nodes either. I am trying not to be a
>>>>>>>> smart alleck or snooty here, but honestly, you really are failing to
>>>>>>>> understand how silly this sounds.
>
> Unfortunately, Ruben seems to have gone incommunicado for an indefinite
> period of time, and he may never see the following explanation:
>
>>>>>>> Harshman is thoroughly committed to the reigning orthodoxy in systematics,
>>>>>>> which dictates that ALL species be put at branch tips = end nodes.
>>>>>>>
>>>>>>> [It also happens to use "nodes" exclusively for "internal nodes" -- hence your use
>>>>>>> of "node" for what he calls "branch tips" is unintelligible to Harshman.]
>>>>>
>>>>>> You aren't reading. The term is "terminal node", as opposed to "internal
>>>>>> node".
>>>>>
>>>>> I have been reading Gould, inter alia:
>>>>>
>>>>> "The extreme rarity of transitional forms in the fossil record persist as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils."
>>>>> --Stephen J. Gould - "Evolution's Erratic Pace," _Natural History_,vol. 86(5) (May 1987): pp. 12-16, at p. 14 Reprinted in _The Panda's Thumb_, pp. 181-182.
>>>>>
>>>>> Note, tips AND nodes. Granted, this was before the orthodoxy started to reign
>>>>> in earnest on the following year, with the final victory in the cladist wars.
>>>
>>>> Gould was writing for a lay audience and wasn't a systematist in any
>>>> case.
>>>
>>> However, he was a biological polymath with a keen mind.
>
>> True, but he wasn't that up on phylogenetic methods.
>
> Methods of constructing phylogenetic trees are irrelevant
> to the issue at hand, which is that these trees are designed to implicitly
> deny direct ancestry to every single pair of taxa since the beginning of life on earth.

It's relevant to your Gould quote, though. If Gould thinks that "node"
means only "internal node" in systematics, then he's wrong, and so are
you. Now how would you create a method of constructing trees that
implicitly allows direct ancestry?

(I do know of one such method, continuous track analysis, but nobody to
my knowledge has ever used it. Perhaps you might like it:

https://academic.oup.com/sysbio/article-abstract/44/2/152/1678263.)

>>>> He probably wasn't up on the language used in phylogenetics. On
>>>> the other hand, I am.
>>>
>>> Your use of "branch lengths" below suggests otherwise.
>
>> Not understanding what you mean by that. Are you saying that "branch
>> length" isn't a term used in phylogenetics?
>
> If you had understood what I wrote directly above, and below, instead of shooting
> from the hip, you wouldn't have asked this asinine question.

And if you were at all interested in real dialogue, you would have just
answered the asinine question. But here it is again: What did you mean
by that?

>>>>>>> I don't know whether Harshman would agree to a compromise such as the following:
>>>>>>> modify Hunt's nicely branching tree to a "thorn tree" where all prime ancestor candidates
>>>>>>> are connected to the tree by as small a thorn as feasible, with a label of 0 (zero) to indicate
>>>>>>> the complete lack of disqualifying characters.
>>>>>
>>>>>> This would be the natural result of any usual phylogenetic analysis of
>>>>>> such taxa.
>>>>>
>>>>> Oh, really? including the part about "thorns" as opposed to longish branches?
>
> It turns out, far below, that "usual" means "molecular" and is useless for
> the kind of project I envision above.

This just isn't true. The usual also applies to morphological and even
fossil analyses.

>>>> Yes, really. Do you understand what branch lengths represent?
>
>>> Are you sure you know what you are talking about? In ALL the detailed
>>> trees that we've talked about this year, branch lengths in the LITERAL
>>> sense have to do with time elapsed. NONE of the numbers labeling
>>> segments of those branches has anything to do with numbers
>>> of apomorphies. Most numerical labels have to do with bootstrap values, and in
>>> the last case below they give mya to the nearest 100,000 years.
>
>> This is sometimes the case.
>
> "sometimes" seems to be a huge understatement.

You don't really have a very large sample in order to make such claims.

>> Branch lengths can be scaled to number of
>> changes, to time, or to nothing at all. But in the case we were talking
>> about, it's the former. Would you like to see examples of such trees?
>
> You are shooting from the hip again without reading further.
> You gave one below [keyword: phylogram]. Unfortunately,
> none of the branch lengths is anywhere near 0, so it doesn't
> really answer my question.

Sorry, what question? Your supposed compromise? If there were an actual
zero-length branch and you printed out the results of an analysis that
found that, you would get a tree that showed a zero-length branch. No
need for any compromise. But of course Hunt's tree was not based on an
explicit data set.

> Besides, what kept you from producing SEVERAL one reply earlier?
> Why do you want to drag the discussion out, unlike me, who provided FIVE
> examples *immediately*?

Are you asking for an example? I didn't previously see the need for one,
since it seems obvious what it would look like.

>> They're pretty common. Further, even when branch lengths aren't
>> displayed in a figure, the analysis used to construct the figure does
>> come up with branch lengths that represent the number of changes.
>
> Finally, you are using "branch lengths" literally. But I'd still love to SEE
> (as opposed to being told by you that it has been done)
> how they manage a branch length that represents 0 apomorphies.

I have always used "branch lengths" literally. But OK, here: Harshman
J., Huddleston C.J., Bollback J., Parsons T.M., Braun M.J. True and
false gharials: A nuclear gene phylogeny of Crocodylia. Systematic
Biology 2003; 52:386-402.

In Fig. 2, the branch separating Crocodylus cataphractus from its common
ancestor with Osteolaemus tetraspis has a length of zero.

>>> Here they are:
>>>
>>> fig. 5 in:
>>> https://www.nature.com/articles/s41598-022-15535-6
>>> branch lengths are governed by time-calibration based on stratigraphic record
>>> [in epochs, not mya]
>
>> Correct.
>
>>> fig. 18 in paper coauthored by Mickey Mortimer:
>>> https://peerj.com/articles/7247/?td=bl&fbclid=IwAR09VFddJNY8v0rvmEh9HmtINsJLScQj0B98UsoKEbTjMMNZLTdxZyA4h4w#systematic
>> Note that in Fig. 17 the branch lengths mean nothing.
>
> That's why I didn't talk about Fig. 17. Duh.
>
>>> Fig. 1 in https://academic.oup.com/gbe/article/9/9/2308/4095375
>>> works as described, except that there is no explicit scale at top or bottom
>> Not sure what "as described" means, but the branches in that tree are
>> scaled by number of changes, if that's what you mean. (Incidentally,
>> that's sometimes called a phylogram to distinguish from an unscaled
>> cladogram.)
>
> Correct, now that I am looking more closely. But the shortest branch lengths
> go to Homo sapiens vis a vis Pan paniscus, and to the walrus vis a vis sea lions.
> So we are very far from a "thorn tree".

I've held off replying to this post of yours all this time, John, in
the hopes of keeping things reasonably civil. But it is kid stuff
compared to some of your behavior on the thread, "Where's Erik,"
these last three days, so there is no point in letting it go unremarked on any longer.

On Monday, September 5, 2022 at 8:07:12 PM UTC-4, John Harshman wrote:
> On 9/5/22 3:51 PM, Peter Nyikos wrote:
> > On Monday, September 5, 2022 at 2:50:32 PM UTC-4, John Harshman wrote:
> >> On 9/5/22 11:42 AM, Peter Nyikos wrote:
> >
> >>> As I looked back yesterday on some 2016 threads in s.b.p. when it was at the height of what I call
> >>> "an oasis of civilization," I came across a long exchange between Ruben Safir
> >>> [who often went under the byline Popping mad, as he does now]
> >>> and John Harshman, which I joined near the end. John and Ruben
> >>> were unable to communicate fruitfully, because John was stuck
> >>> in a dichotomy between two ways of classifying organisms:
> >>> the cladistic and the phenetic.
> >
> >> Needless to say, I reject your characterization of that argument.
> >
> > Automatic reflex reaction noted.

> Try to engage with my argument rather than just characterizing it.

You call what you wrote up there an argument??

> > You obviously haven't looked at the thread in over six years,
> > not with Giganews archives only going back a month.

> Of course I haven't. But I know my own opinions.

About yourself, based on all of the above. And they seem -- to put it mildly -- rather egotistic.

> > But I'll help you. Here is the url for the entire thread.
> > https://groups.google.com/g/sci.bio.paleontology/c/sFY6QxipSb4/m/T0QLNBF0AQAJ
> >
> > Happy surfing up and down the 148 posts. Here is a note I made on one of them:
> >
> > "Harshman is stuck in a false dichotomy between cladistics and phenetics"
> > Apr 14, 2016, 5:03:15 PM
> >
> > You may want to start there.
> >
> >
> > See you tomorrow with the post that addresses this false dichotomy of yours.

> Why begin with a personal attack? What's the point?

I only began a personal attack this time around.

If you think saying that you had been stuck in a false dichotomy is an attack,
you are taking things way too personally. The cladistic wars were
stuck in the same dichotomy. Were you too wrapped up in looking for
personal affronts to notice that herd of elephants in the room?

Sheesh.

But now, contrast your "emotional hemophiliac" behavior with
your full-bore gaslighting allegation of "megalomania" with which
I dealt two days after you wrote the above:

https://groups.google.com/g/talk.origins/c/exNELbZoE1k/m/bHyj_wb3CQAJ
Re: Hole In One
Sep 7, 2022, 10:10:05 AM

Needless to say, you haven't thought of a good comeback in
all this time. Did you think jillery let you off the hook with
the following direct reply to my linked post?

https://groups.google.com/g/talk.origins/c/exNELbZoE1k/m/TidKscYmCgAJ

Do you really want to associate yourself with the staggeringly
dishonest way jillery did it?

Peter Nyikos

PS One thing is for sure: jillery made it clear that she will
back you to the hilt no matter how despicably you behave towards me.

On 9/30/22 4:20 PM, Peter Nyikos wrote:
> I've held off replying to this post of yours all this time, John, in
> the hopes of keeping things reasonably civil. But it is kid stuff
> compared to some of your behavior on the thread, "Where's Erik,"
> these last three days, so there is no point in letting it go unremarked on any longer.
>
> On Monday, September 5, 2022 at 8:07:12 PM UTC-4, John Harshman wrote:
>> On 9/5/22 3:51 PM, Peter Nyikos wrote:
>>> On Monday, September 5, 2022 at 2:50:32 PM UTC-4, John Harshman wrote:
>>>> On 9/5/22 11:42 AM, Peter Nyikos wrote:
>>>
>>>>> As I looked back yesterday on some 2016 threads in s.b.p. when it was at the height of what I call
>>>>> "an oasis of civilization," I came across a long exchange between Ruben Safir
>>>>> [who often went under the byline Popping mad, as he does now]
>>>>> and John Harshman, which I joined near the end. John and Ruben
>>>>> were unable to communicate fruitfully, because John was stuck
>>>>> in a dichotomy between two ways of classifying organisms:
>>>>> the cladistic and the phenetic.
>>>
>>>> Needless to say, I reject your characterization of that argument.
>>>
>>> Automatic reflex reaction noted.
>
>> Try to engage with my argument rather than just characterizing it.
>
> You call what you wrote up there an argument??

No, I call the argument I had with Ruben an argument. The one you just
characterized without engaging with.

>>> You obviously haven't looked at the thread in over six years,
>>> not with Giganews archives only going back a month.
>
>> Of course I haven't. But I know my own opinions.
>
> About yourself, based on all of the above. And they seem -- to put it mildly -- rather egotistic.

??

>>> But I'll help you. Here is the url for the entire thread.
>>> https://groups.google.com/g/sci.bio.paleontology/c/sFY6QxipSb4/m/T0QLNBF0AQAJ
>>>
>>> Happy surfing up and down the 148 posts. Here is a note I made on one of them:
>>>
>>> "Harshman is stuck in a false dichotomy between cladistics and phenetics"
>>> Apr 14, 2016, 5:03:15 PM
>>>
>>> You may want to start there.
>>>
>>>
>>> See you tomorrow with the post that addresses this false dichotomy of yours.
>
>> Why begin with a personal attack? What's the point?
>
> I only began a personal attack this time around.
>
> If you think saying that you had been stuck in a false dichotomy is an attack,
> you are taking things way too personally. The cladistic wars were
> stuck in the same dichotomy. Were you too wrapped up in looking for
> personal affronts to notice that herd of elephants in the room?

Does any of this trash talk serve a legitimate purpose?

Does any of the off-topic whatever-it-is that follows below?

> But now, contrast your "emotional hemophiliac" behavior with
> your full-bore gaslighting allegation of "megalomania" with which
> I dealt two days after you wrote the above:
>
> https://groups.google.com/g/talk.origins/c/exNELbZoE1k/m/bHyj_wb3CQAJ
> Re: Hole In One
> Sep 7, 2022, 10:10:05 AM
>
> Needless to say, you haven't thought of a good comeback in
> all this time. Did you think jillery let you off the hook with
> the following direct reply to my linked post?
>
> https://groups.google.com/g/talk.origins/c/exNELbZoE1k/m/TidKscYmCgAJ
>
> Do you really want to associate yourself with the staggeringly
> dishonest way jillery did it?
>
>
> Peter Nyikos
>
> PS One thing is for sure: jillery made it clear that she will
> back you to the hilt no matter how despicably you behave towards me.

On Friday, September 30, 2022 at 7:39:47 PM UTC-4, John Harshman wrote:
> On 9/30/22 4:20 PM, Peter Nyikos wrote:
> > I've held off replying to this post of yours all this time, John, in
> > the hopes of keeping things reasonably civil. But it is kid stuff
> > compared to some of your behavior on the thread, "Where's Erik,"
> > these last three days, so there is no point in letting it go unremarked on any longer.
> >
> > On Monday, September 5, 2022 at 8:07:12 PM UTC-4, John Harshman wrote:
> >> On 9/5/22 3:51 PM, Peter Nyikos wrote:
> >>> On Monday, September 5, 2022 at 2:50:32 PM UTC-4, John Harshman wrote:
> >>>> On 9/5/22 11:42 AM, Peter Nyikos wrote:
> >>>
> >>>>> As I looked back yesterday on some 2016 threads in s.b.p. when it was at the height of what I call
> >>>>> "an oasis of civilization," I came across a long exchange between Ruben Safir
> >>>>> [who often went under the byline Popping mad, as he does now]
> >>>>> and John Harshman, which I joined near the end. John and Ruben
> >>>>> were unable to communicate fruitfully, because John was stuck
> >>>>> in a dichotomy between two ways of classifying organisms:
> >>>>> the cladistic and the phenetic.
> >>>
> >>>> Needless to say, I reject your characterization of that argument.
> >>>
> >>> Automatic reflex reaction noted.
> >
> >> Try to engage with my argument rather than just characterizing it.
> >
> > You call what you wrote up there an argument??

> No, I call the argument I had with Ruben an argument.

I think I've made my point further down in the post
to which you were replying on September 5. Keep reading.

> The one you just characterized without engaging with.

I did, below, by telling you the url for the whole thread
and identifying a specific post on it.

> >>> You obviously haven't looked at the thread in over six years,
> >>> not with Giganews archives only going back a month.
> >
> >> Of course I haven't. But I know my own opinions.
> >
> > About yourself, based on all of the above. And they seem -- to put it mildly -- rather egotistic.
> ??

Sight unseen, you assumed that my description was incorrect. But you've accepted the
results of "the cladist wars" even though they were all about cladistics vs. phenetics.

But what I documented below is even more symptomatic of egotism.

> >>> But I'll help you. Here is the url for the entire thread.
> >>> https://groups.google.com/g/sci.bio.paleontology/c/sFY6QxipSb4/m/T0QLNBF0AQAJ
> >>>
> >>> Happy surfing up and down the 148 posts. Here is a note I made on one of them:
> >>>
> >>> "Harshman is stuck in a false dichotomy between cladistics and phenetics"
> >>> Apr 14, 2016, 5:03:15 PM
> >>>
> >>> You may want to start there.
> >>>
> >>>
> >>> See you tomorrow with the post that addresses this false dichotomy of yours.

It took you a while to find the post, because you didn't realize how deeply
cladistics vs. phenetics was embedded in it. But I think I made you see that.

But you couldn't wait for it on the 5th:
> >> Why begin with a personal attack? What's the point?
> >
> > I only began a personal attack this time around.
> >
> > If you think saying that you had been stuck in a false dichotomy is an attack,
> > you are taking things way too personally. The cladistic wars were
> > stuck in the same dichotomy. Were you too wrapped up in looking for
> > personal affronts to notice that herd of elephants in the room?

> Does any of this trash talk serve a legitimate purpose?

Looks like we can add "trash talk" to a sentence I wrote earlier on this thread:

"You keep coming across as someone with a childish belief in the magic of words
(grudge, traitor, megalomania, paranoid, etc.) whose usage you stretch well past the breaking point."
-- https://groups.google.com/g/sci.bio.paleontology/c/slPe9xLMxkk/m/igSUqzk8FAAJ

> Does any of the off-topic whatever-it-is that follows below?

Both it and what you whined about above serve the purpose of finding out
how flagrantly you adhere to double standards.

Are you man enough to admit that what I described and documented below
was you indulging in trash talk? and that it was wrong for you to do it?

> > But now, contrast your "emotional hemophiliac" behavior with
> > your full-bore gaslighting allegation of "megalomania" with which
> > I dealt two days after you wrote the above:
> >
> > https://groups.google.com/g/talk.origins/c/exNELbZoE1k/m/bHyj_wb3CQAJ
> > Re: Hole In One
> > Sep 7, 2022, 10:10:05 AM

Peter Nyikos

On 10/4/22 4:24 PM, Peter Nyikos wrote:

I'm only responding to this because you will complain if I don't. I have
snipped all the off-topic parts and find there's nothing left. If you
would like to compose a post that is both a) on-topic and b) doesn't
reply to multiple levels of nesting, I will be glad to respond similarly.