Paraphyly vs. Monophyly

[John Harshman]

Rather than clog up a thread on pterosaurs, let's argue about the
benefits of paraphyly vs. monophyly here. There are several
distinguishable issues:

1. Can paraphyletic groups be more useful in classification than strict
adherence to monophyly?

2. Should particular fossil "species" be declared to be ancestors or
ancestor candidates, and if so, what is gained?

3. Is it useful to declare higher taxa ancestral to other taxa?

4. Are "evolutionary trees" (in which taxa are ancestral, either by
placing species at internal nodes or by having taxa emerge from
"bubbles") ever more useful than phylogenetic trees (i.e. cladograms
with or without meaningful branch lengths)?

Discuss. My answers of course would be no, no, no, and no.

[Oxyaena]

For the record I agree with all of your answers.

[erik simpson]

There aren't very many of us even present here any more, and I think we all know
what everyone else thinks about these (valid) considerations. The "war" in
paleontology more generally was fought a long time ago, and the outcome is
well-known. We are also all aware of the dissenter among us, whose postions
seem not to have varied significantly since 1945 (an important publication date
for Romer's tome). This can't be, because our dissenter hadn't been born at
that time, or was still an infant. He hasn't mentioned overlapping paraphyletic groups for a while, so perhaps his opinions have evolved over time, but the
recent instances of his credo sound much the same as the many repetitions he's
posted before.

If there is more to discuss about pterosaurs, let's do that instead. This
thread will either die quickly if he ignores it, or become ugly and rancorous,
go on for a long time and get nowhere.

[Oxyaena]

I'd have to agree with you on that.

[John Harshman]

On 8/2/18 8:15 AM, erik simpson wrote:
> On Wednesday, August 1, 2018 at 8:28:36 PM UTC-7, John Harshman wrote:
>> Rather than clog up a thread on pterosaurs, let's argue about the
>> benefits of paraphyly vs. monophyly here. There are several
>> distinguishable issues:
>>
>> 1. Can paraphyletic groups be more useful in classification than strict
>> adherence to monophyly?
>>
>> 2. Should particular fossil "species" be declared to be ancestors or
>> ancestor candidates, and if so, what is gained?
>>
>> 3. Is it useful to declare higher taxa ancestral to other taxa?
>>
>> 4. Are "evolutionary trees" (in which taxa are ancestral, either by
>> placing species at internal nodes or by having taxa emerge from
>> "bubbles") ever more useful than phylogenetic trees (i.e. cladograms
>> with or without meaningful branch lengths)?
>>
>> Discuss. My answers of course would be no, no, no, and no.
>
> There aren't very many of us even present here any more, and I think we all know
> what everyone else thinks about these (valid) considerations.

I'm merely asking Peter if he can make a valid argument for his claims,
and in a thread actually designed for that purpose. Why complain in
advance of the facts?

[erik simpson]

I'm not really complaining. If he wants to hold forth on this subject, fine;
here's the place to do it. I don't expect any new revelations or arguments on
this subject.

[Peter Nyikos]

On Wednesday, August 1, 2018 at 11:28:36 PM UTC-4, John Harshman wrote:
> Rather than clog up a thread on pterosaurs, let's argue about the
> benefits of paraphyly vs. monophyly here. There are several
> distinguishable issues:
>
> 1. Can paraphyletic groups be more useful in classification than strict
> adherence to monophyly?

Poorly worded. Ever since 2002 all I have ever argued for was for
cladophiles like you not to ban paraphyletic groups, but to admit
them side by side with monophyletic ones, because they also
contribute to our understanding of evolution.

> 2. Should particular fossil "species" be declared to be ancestors or
> ancestor candidates, and if so, what is gained?
>
> 3. Is it useful to declare higher taxa ancestral to other taxa?

Also poorly worded. It is not the higher taxa, but species not
yet discovered that are WITHIN those taxa that are ancestral
even to such spectacular taxa as tetrapoda. We already have two
genera, Tiktaalik and another whose name begins with E that are
very likely in the same family, maybe even subfamily (as the old-timers
reckoned these things, as an actual ancestor of all members of
the crown group Tetrapoda, and many terrestrial vertebrates outside it.

> 4. Are "evolutionary trees" (in which taxa are ancestral, either by
> placing species at internal nodes or by having taxa emerge from
> "bubbles") ever more useful than phylogenetic trees (i.e. cladograms
> with or without meaningful branch lengths)?
>
> Discuss. My answers of course would be no, no, no, and no.

Sans discussion, I see.

As you know, I have given rational arguments for all of the above, and
now I'd like to see rational arguments for these negative answers.

And I don't mean emotional arguments like the following, which
only lends support to the thesis that your negative answers
are ideologically and not scientifically based.

I didn't read all the way through, since the cladophobe bullshit
infested every corner of my screen I quickly clicked out of it lest I
get your disease.
https://groups.google.com/d/msg/sci.bio.paleontology/RNINuDOndSM/cy3gGiLiBQAJ

I had written:
By the way, you haven't responded to my post of yesterday
in reply to Ruben Safir, even though there was actual
paleontology at the end, not just systematics. Can you say "double
standard"?
--- from the Pterosaur thread to which you refer at the beginning

And the response was what you are reading above.

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

[John Harshman]

On 8/7/18 5:42 PM, Peter Nyikos wrote:
> On Wednesday, August 1, 2018 at 11:28:36 PM UTC-4, John Harshman wrote:
>> Rather than clog up a thread on pterosaurs, let's argue about the
>> benefits of paraphyly vs. monophyly here. There are several
>> distinguishable issues:
>>
>> 1. Can paraphyletic groups be more useful in classification than strict
>> adherence to monophyly?
>
> Poorly worded. Ever since 2002 all I have ever argued for was for
> cladophiles like you not to ban paraphyletic groups, but to admit
> them side by side with monophyletic ones, because they also
> contribute to our understanding of evolution.

It isn't quite clear what "side by side" means. Are you proposing two
parallel classification systems, one with strict monophyly and one
allowing paraphyly? To me, that just seems redundant. If that's what you
mean.

>> 2. Should particular fossil "species" be declared to be ancestors or
>> ancestor candidates, and if so, what is gained?
>>
>> 3. Is it useful to declare higher taxa ancestral to other taxa?
>
> Also poorly worded. It is not the higher taxa, but species not
> yet discovered that are WITHIN those taxa that are ancestral
> even to such spectacular taxa as tetrapoda. We already have two
> genera, Tiktaalik and another whose name begins with E that are
> very likely in the same family, maybe even subfamily (as the old-timers
> reckoned these things, as an actual ancestor of all members of
> the crown group Tetrapoda, and many terrestrial vertebrates outside it.

How would you determine if these species are in the same family or
subfamily as the ancestor? And what is gained?

>> 4. Are "evolutionary trees" (in which taxa are ancestral, either by
>> placing species at internal nodes or by having taxa emerge from
>> "bubbles") ever more useful than phylogenetic trees (i.e. cladograms
>> with or without meaningful branch lengths)?
>>
>> Discuss. My answers of course would be no, no, no, and no.
>
> Sans discussion, I see.

That's because I would like to hear your arguments. Please give your
arguments.

> As you know, I have given rational arguments for all of the above, and
> now I'd like to see rational arguments for these negative answers.

Sorry, but I do not recall you giving any rational arguments. We
probably disagree on what's rational. I was inviting you to give it your
best shot.

> And I don't mean emotional arguments like the following, which
> only lends support to the thesis that your negative answers
> are ideologically and not scientifically based.
>
> I didn't read all the way through, since the cladophobe bullshit
> infested every corner of my screen I quickly clicked out of it lest I
> get your disease.
> https://groups.google.com/d/msg/sci.bio.paleontology/RNINuDOndSM/cy3gGiLiBQAJ

How does this lend support to any thesis about me? I didn't say that.
That would appear to be Oxyaena.

> I had written:
> By the way, you haven't responded to my post of yesterday
> in reply to Ruben Safir, even though there was actual
> paleontology at the end, not just systematics. Can you say "double
> standard"?
> --- from the Pterosaur thread to which you refer at the beginning
>
> And the response was what you are reading above.

Not my response, though.

[Oxyaena]

I wrote it, it has nothing to do with this thread, ergo usual Nyikosian
drivel, and it was in response to his irrational response to my initial
post, which was extremely polite (he likes to leave that out) on the
Pterosaur thread. Ignore when he does this, it only feeds the troll.

[Oxyaena]

On 8/7/2018 11:13 PM, John Harshman wrote:

I should also add that he left out *why* I disagree with him on this
issue, namely that Linnaean taxonomy doesn't do a good job of
representing evolutionary relationships, cladistics does a far better
job at it, since Linnaean taxonomy would place chimps and other apes in
Pongo, while cladistics does a better job at accurately showing
evolutionary relationships between taxa, so chimps and humans will be
placed in a clade, with gorillas as an offshoot of the clade and
orangutans being the sister group to the clade.

In short, he's being a dishonest prick and should be ignored, as I am
refusing to respond to him since he gets on my nerves. I wrote my
flippant remark after several posts engaging him on this issue, my
patience wore thin, I had explained to him in-depth why he was wrong
*politely* several times, and he kept up his bullshit like I had never
even wrote what I did. You should discount him mentioning me, it has
nothing to do with you and is only him being a libelous piece of shit.

It's also the same thread where I read him the riot act saying I will no
longer play his games. You should do the same.

[Peter Nyikos]

On Thursday, August 2, 2018 at 4:34:36 PM UTC-4, erik simpson wrote:
> On Thursday, August 2, 2018 at 8:44:39 AM UTC-7, John Harshman wrote:
> > On 8/2/18 8:15 AM, erik simpson wrote:
> > > On Wednesday, August 1, 2018 at 8:28:36 PM UTC-7, John Harshman wrote:
> > >> Rather than clog up a thread on pterosaurs, let's argue about the
> > >> benefits of paraphyly vs. monophyly here. There are several
> > >> distinguishable issues:
> > >>
> > >> 1. Can paraphyletic groups be more useful in classification than strict
> > >> adherence to monophyly?
> > >>
> > >> 2. Should particular fossil "species" be declared to be ancestors or
> > >> ancestor candidates, and if so, what is gained?
> > >>
> > >> 3. Is it useful to declare higher taxa ancestral to other taxa?
> > >>
> > >> 4. Are "evolutionary trees" (in which taxa are ancestral, either by
> > >> placing species at internal nodes or by having taxa emerge from
> > >> "bubbles") ever more useful than phylogenetic trees (i.e. cladograms
> > >> with or without meaningful branch lengths)?
> > >>
> > >> Discuss. My answers of course would be no, no, no, and no.
> > >
> > > There aren't very many of us even present here any more, and I think we all know
> > > what everyone else thinks about these (valid) considerations.

Fallacy of begging the question.

> > I'm merely asking Peter if he can make a valid argument for his claims,
> > and in a thread actually designed for that purpose. Why complain in
> > advance of the facts?
>
> I'm not really complaining. If he wants to hold forth on this subject, fine;
> here's the place to do it. I don't expect any new revelations or arguments on
> this subject.

Especially not from John or you or Oxyaena, apparently.
"Jump on the bandwagon, or be left in the dustbin of history"
is not a valid argument for the real claim the three of you are making.

The real claim is exemplified by what the Subject line should have been:

Subject: Prohibition of paraphyly vs toleration thereof

... in what has replaced a classification where the overwhelming
majority of taxa were hypothesized as monophylic, even in the days of Romer.

That classification has been consigned to the dustbin of history without
a fair hearing. The "cow - lungfish - trout" brouhaha that seems
to have been the decisive battle in the war that resulted in the
banishment of paraphyletic taxa was conducted with a cladophile-serving
definition of "more related". And the traditional systematists
don't seem to have realized how biased it was against them.

I've been through an argument about that bizarre (when compared to the
everyday meaning of "more related") definition with Oxyaena.
That neither you nor John saw fit to enter into that argument
is your loss, not mine. The upshot is that John started a new
thread that doesn't even hint at this argument.


Peter Nyikos
Professor of Mathematics -- standard disclaimer--

[Oxyaena]

> Especially not from me.

Fixed it for you.

> "Jump on the bandwagon, or be left in the dustbin of history"
> is not a valid argument for the real claim the three of you are making.
>
> The real claim is exemplified by what the Subject line should have been:
>
> Subject: Prohibition of paraphyly vs toleration thereof
>
> ... in what has replaced a classification where the overwhelming
> majority of taxa were hypothesized as monophylic, even in the days of Romer.
>
> That classification has been consigned to the dustbin of history without
> a fair hearing. The "cow - lungfish - trout" brouhaha that seems
> to have been the decisive battle in the war that resulted in the
> banishment of paraphyletic taxa was conducted with a cladophile-serving
> definition of "more related". And the traditional systematists
> don't seem to have realized how biased it was against them.

Let the Ranting of the Cladophobe commence! Seriously, your dismissal of
the term "more related" is especially idiotic in light of your support
for Linnaean taxonomy: "No one would argue that Mitochondrial Eve is
more closely related to us than to her own mother." Come on, Peter, at
least be consistent with your bullshit.

>
> I've been through an argument about that bizarre (when compared to the
> everyday meaning of "more related") definition with Oxyaena.
> That neither you nor John saw fit to enter into that argument
> is your loss, not mine. The upshot is that John started a new
> thread that doesn't even hint at this argument.

You're an idiot. I have no interest in repeating myself to you over why
cladistics is a better system at representing evolutionary relationships
than Linnaean taxonomy is.

HAND

[Peter Nyikos]

On Tuesday, August 7, 2018 at 11:13:50 PM UTC-4, John Harshman wrote:
> On 8/7/18 5:42 PM, Peter Nyikos wrote:
> > On Wednesday, August 1, 2018 at 11:28:36 PM UTC-4, John Harshman wrote:
> >> Rather than clog up a thread on pterosaurs, let's argue about the
> >> benefits of paraphyly vs. monophyly here. There are several
> >> distinguishable issues:
> >>
> >> 1. Can paraphyletic groups be more useful in classification than strict
> >> adherence to monophyly?
> >
> > Poorly worded. Ever since 2002 all I have ever argued for was for
> > cladophiles like you not to ban paraphyletic groups, but to admit
> > them side by side with monophyletic ones, because they also
> > contribute to our understanding of evolution.
>
> It isn't quite clear what "side by side" means.

It ought to be clear. I've explained it at least once a year, on the
average, since 2010. Evidently all those comparisons with the
side by side Dewey Decimal System and the Library of Congress system
"went in one ear and out the other," as my grade school and high school
teachers put it. [This was in the days before "middle school" became
a widespread institution.]

> Are you proposing two
> parallel classification systems, one with strict monophyly and one
> allowing paraphyly? To me, that just seems redundant. If that's what you
> mean.

You might make a case for "redundant" wrt those age-old parallel
library systems, but the traditional classification had vastly
different aims. For one, its ideal was a finer and finer narrowing
down of "ancestry". The system you champion has given up altogether
on the concept of ancestry:

> >> 2. Should particular fossil "species" be declared to be ancestors or
> >> ancestor candidates, and if so, what is gained?

For one thing: a concept of "related" that resembles the one
in everyday use. It is like saying "this person is claiming
to be the son of ___________ and we need to go on evaluating
this claim, which thus far has passed every test."

> >> 3. Is it useful to declare higher taxa ancestral to other taxa?
> >
> > Also poorly worded. It is not the higher taxa, but species not
> > yet discovered that are WITHIN those taxa that are ancestral
> > even to such spectacular taxa as tetrapoda. We already have two
> > genera, Tiktaalik and another whose name begins with E that are
> > very likely in the same family, maybe even subfamily (as the old-timers
> > reckoned these things, as an actual ancestor of all members of
> > the crown group Tetrapoda, and many terrestrial vertebrates outside it.
>
> How would you determine if these species are in the same family or
> subfamily as the ancestor?

By continuing to refine the parameters of what constitutes a family.
For instance, "they are in the same family as seen by systematists
specializing in marsupials, but only in the same order as seen
by systematists specializing in ornithology."


> And what is gained?

A statement roughly analogous to "This person is from the MacLane clan"
versus e.g. "This person has pure Celtic ancestry".

>
> >> 4. Are "evolutionary trees" (in which taxa are ancestral, either by
> >> placing species at internal nodes or by having taxa emerge from
> >> "bubbles") ever more useful than phylogenetic trees (i.e. cladograms
> >> with or without meaningful branch lengths)?
> >>
> >> Discuss. My answers of course would be no, no, no, and no.
> >
> > Sans discussion, I see.
>
> That's because I would like to hear your arguments. Please give your
> arguments.

You have shot all of them down with refrains starting with
"I don't see how..." without trying to rationally explain
WHAT may be wrong with my arguments.

> > As you know, I have given rational arguments for all of the above, and
> > now I'd like to see rational arguments for these negative answers.
>
> Sorry, but I do not recall you giving any rational arguments.

You've arbitrarily decreed my numerous scientifically based arguments
to be non-rational.

With such blatant poisoning of the wells, how do you expect me to
do a one-person tango, sans any arguments where YOU stick YOUR
neck out.

> We
> probably disagree on what's rational. I was inviting you to give it your
> best shot.
>
> > And I don't mean emotional arguments like the following, which
> > only lends support to the thesis that your negative answers
> > are ideologically and not scientifically based.
> >
> > I didn't read all the way through, since the cladophobe bullshit
> > infested every corner of my screen I quickly clicked out of it lest I
> > get your disease.
> > https://groups.google.com/d/msg/sci.bio.paleontology/RNINuDOndSM/cy3gGiLiBQAJ
>
> How does this lend support to any thesis about me? I didn't say that.
> That would appear to be Oxyaena.

It was. And you show no sign of disapproval.

As I was hinting above, it takes two to tango.

>
> > I had written:
> > By the way, you haven't responded to my post of yesterday
> > in reply to Ruben Safir, even though there was actual
> > paleontology at the end, not just systematics. Can you say "double
> > standard"?
> > --- from the Pterosaur thread to which you refer at the beginning
> >
> > And the response was what you are reading above.
>
> Not my response, though.

What is YOUR excuse for not entering into my argument with Ruben?

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

[John Harshman]

On 8/8/18 6:28 AM, Peter Nyikos wrote:
> On Tuesday, August 7, 2018 at 11:13:50 PM UTC-4, John Harshman wrote:
>> On 8/7/18 5:42 PM, Peter Nyikos wrote:
>>> On Wednesday, August 1, 2018 at 11:28:36 PM UTC-4, John Harshman wrote:
>>>> Rather than clog up a thread on pterosaurs, let's argue about the
>>>> benefits of paraphyly vs. monophyly here. There are several
>>>> distinguishable issues:
>>>>
>>>> 1. Can paraphyletic groups be more useful in classification than strict
>>>> adherence to monophyly?
>>>
>>> Poorly worded. Ever since 2002 all I have ever argued for was for
>>> cladophiles like you not to ban paraphyletic groups, but to admit
>>> them side by side with monophyletic ones, because they also
>>> contribute to our understanding of evolution.
>>
>> It isn't quite clear what "side by side" means.
>
> It ought to be clear. I've explained it at least once a year, on the
> average, since 2010. Evidently all those comparisons with the
> side by side Dewey Decimal System and the Library of Congress system
> "went in one ear and out the other," as my grade school and high school
> teachers put it. [This was in the days before "middle school" became
> a widespread institution.]

You are being very uncommunicative lately. Consider leaving out all the
accusations and gotchas and just responding directly to the point.

>> Are you proposing two
>> parallel classification systems, one with strict monophyly and one
>> allowing paraphyly? To me, that just seems redundant. If that's what you
>> mean.
>
> You might make a case for "redundant" wrt those age-old parallel
> library systems, but the traditional classification had vastly
> different aims. For one, its ideal was a finer and finer narrowing
> down of "ancestry".

I don't think that's actually true. How does "Reptilia", for example,
result in a finer narrowing down of ancestry for mammals and birds?

> The system you champion has given up altogether
> on the concept of ancestry:

Yes, with good reason; it's not something we can determine.

And how can two parallel classifications fail to result in confusion?

>>>> 2. Should particular fossil "species" be declared to be ancestors or
>>>> ancestor candidates, and if so, what is gained?
>
> For one thing: a concept of "related" that resembles the one
> in everyday use. It is like saying "this person is claiming
> to be the son of ___________ and we need to go on evaluating
> this claim, which thus far has passed every test."

I don't see an advantage to that concept. And it doesn't work anyway.
With paraphyletic taxa, there must always be a point at which closest
relatives (by your preferred concept) will be separated into different
families, orders, and classes.

>>>> 3. Is it useful to declare higher taxa ancestral to other taxa?
>>>
>>> Also poorly worded. It is not the higher taxa, but species not
>>> yet discovered that are WITHIN those taxa that are ancestral
>>> even to such spectacular taxa as tetrapoda. We already have two
>>> genera, Tiktaalik and another whose name begins with E that are
>>> very likely in the same family, maybe even subfamily (as the old-timers
>>> reckoned these things, as an actual ancestor of all members of
>>> the crown group Tetrapoda, and many terrestrial vertebrates outside it.
>>
>> How would you determine if these species are in the same family or
>> subfamily as the ancestor?
>
> By continuing to refine the parameters of what constitutes a family.
> For instance, "they are in the same family as seen by systematists
> specializing in marsupials, but only in the same order as seen
> by systematists specializing in ornithology."

That seems to me just to add more confusion.

>> And what is gained?
>
> A statement roughly analogous to "This person is from the MacLane clan"
> versus e.g. "This person has pure Celtic ancestry".

That would be identically stated in a cladistic classification, so
doesn't communicate any difference. The analogy must be too rough to
serve your purpose.

>>>> 4. Are "evolutionary trees" (in which taxa are ancestral, either by
>>>> placing species at internal nodes or by having taxa emerge from
>>>> "bubbles") ever more useful than phylogenetic trees (i.e. cladograms
>>>> with or without meaningful branch lengths)?
>>>>
>>>> Discuss. My answers of course would be no, no, no, and no.
>>>
>>> Sans discussion, I see.
>>
>> That's because I would like to hear your arguments. Please give your
>> arguments.
>
> You have shot all of them down with refrains starting with
> "I don't see how..." without trying to rationally explain
> WHAT may be wrong with my arguments.

I would like to see your arguments before explaining what's wrong with
them. Isn't that a reasonable request?

>>> As you know, I have given rational arguments for all of the above, and
>>> now I'd like to see rational arguments for these negative answers.
>>
>> Sorry, but I do not recall you giving any rational arguments.
>
> You've arbitrarily decreed my numerous scientifically based arguments
> to be non-rational.

> With such blatant poisoning of the wells, how do you expect me to
> do a one-person tango, sans any arguments where YOU stick YOUR
> neck out.

I'm just trying to find out what you think supports your position. So
far you have not made any clear arguments. What would be the danger in
doing so?

My argument is that I can't see any benefit in any of the things I
started this thread with; absent benefit, there's no reason to do it.
Refute me by showing the benefit.

>> We
>> probably disagree on what's rational. I was inviting you to give it your
>> best shot.
>>
>>> And I don't mean emotional arguments like the following, which
>>> only lends support to the thesis that your negative answers
>>> are ideologically and not scientifically based.
>>>
>>> I didn't read all the way through, since the cladophobe bullshit
>>> infested every corner of my screen I quickly clicked out of it lest I
>>> get your disease.
>>> https://groups.google.com/d/msg/sci.bio.paleontology/RNINuDOndSM/cy3gGiLiBQAJ
>>
>> How does this lend support to any thesis about me? I didn't say that.
>> That would appear to be Oxyaena.
>
> It was. And you show no sign of disapproval.

I tend not to respond to empty trash talk, either by you or others.

> As I was hinting above, it takes two to tango.

No idea what that means. Perhaps you should do more than hint.

>>> I had written:
>>> By the way, you haven't responded to my post of yesterday
>>> in reply to Ruben Safir, even though there was actual
>>> paleontology at the end, not just systematics. Can you say "double
>>> standard"?
>>> --- from the Pterosaur thread to which you refer at the beginning
>>>
>>> And the response was what you are reading above.
>>
>> Not my response, though.
>
> What is YOUR excuse for not entering into my argument with Ruben?

I don't need an excuse. I enter when I have something interesting to say
or am interested in getting an answer. Since I don't recall what your
argument with Ruben is, I probably had neither reason. You should not
take that an an affront.

[Peter Nyikos]

All the years you posted to talk.origins, you've been exposed to the convention you are misusing below. The universal custom is to put the
change in brackets: "Especially not from [me]." is the way it would go.

> Fixed it for you.

I had no illusions about the following "promise" you made after
I caught you doing multiple slanders, but even I didn't think
you would break it so soon:

I`m not going to dignify your bullshit
anymore by responding to you, consider this my last response to you,
Peter, period.

>
> > "Jump on the bandwagon, or be left in the dustbin of history"
> > is not a valid argument for the real claim the three of you are making.

And I see no sign of anyone here giving any other argument
against the stand I took below:

> > The real claim is exemplified by what the Subject line should have been:
> >
> > Subject: Prohibition of paraphyly vs toleration thereof
> >
> > ... in what has replaced a classification where the overwhelming
> > majority of taxa were hypothesized as monophylic, even in the days of Romer.
> >
> > That classification has been consigned to the dustbin of history without
> > a fair hearing. The "cow - lungfish - trout" brouhaha that seems
> > to have been the decisive battle in the war that resulted in the
> > banishment of paraphyletic taxa was conducted with a cladophile-serving
> > definition of "more related". And the traditional systematists
> > don't seem to have realized how biased it was against them.
>
> Let the Ranting of the Cladophobe commence!

There never was any ranting by me on the subject, and there never
will be.

"Cladophobe" is insincere because it implies an unwarranted
fear of cladistic classification. I'm perfectly OK with it,
and you know that.

> Seriously, your dismissal of
> the term "more related" is especially idiotic in light of your support
> for Linnaean taxonomy:

Side by side with the only one YOU can stomach, let it not be forgot.

>"No one would argue that Mitochondrial Eve is
> more closely related to us than to her own mother." Come on, Peter, at
> least be consistent with your bullshit.

I am perfectly consistent, and if you can't see that, you need
to see a psychiatrist.

But I think you do see that, and are thus being completely
insincere about accusing me of inconsistency.

> >
> > I've been through an argument about that bizarre (when compared to the
> > everyday meaning of "more related") definition with Oxyaena.

And the Mitochondrial Eve analogy is designed to show just
HOW bizarre it is. That's consistency, you insufferable troll.

> > That neither you nor John saw fit to enter into that argument
> > is your loss, not mine. The upshot is that John started a new
> > thread that doesn't even hint at this argument.
>
> You're an idiot.

I think I see why you broke your "promise" so soon: you could make this
illogical insult without what I wrote having been a "bygone".

> I have no interest in repeating myself to you over why
> cladistics is a better system at representing evolutionary relationships
> than Linnaean taxonomy is.

It's nice to see that even you have limits where broken record routines
are concerned. I'm referring to endless repetitions
of "better showing of relationships" with no attempt to address
the revolutionary nature of the cladophile way with the word
"relationships."

By the way, you DO realize that you DID repeat yourself, don't you?
But perhaps this is the last time, yes?


> HAND

The same to you, with the (probably forlorn) hope that you will
make good on the message implied by your "forgery" of what I wrote.

> > Peter Nyikos
> > Professor of Mathematics -- standard disclaimer--
> > University of South Carolina

http://www.math.sc.edu/~nyikos
> >

[Oxyaena]

Let's add "slander" to the list of words you don't know the meaning of
but keep using anyways.

>
> I`m not going to dignify your bullshit
> anymore by responding to you, consider this my last response to you,
> Peter, period.
>
>>
>>> "Jump on the bandwagon, or be left in the dustbin of history"
>>> is not a valid argument for the real claim the three of you are making.
>
> And I see no sign of anyone here giving any other argument
> against the stand I took below:
>
>>> The real claim is exemplified by what the Subject line should have been:
>>>
>>> Subject: Prohibition of paraphyly vs toleration thereof
>>>
>>> ... in what has replaced a classification where the overwhelming
>>> majority of taxa were hypothesized as monophylic, even in the days of Romer.
>>>
>>> That classification has been consigned to the dustbin of history without
>>> a fair hearing. The "cow - lungfish - trout" brouhaha that seems
>>> to have been the decisive battle in the war that resulted in the
>>> banishment of paraphyletic taxa was conducted with a cladophile-serving
>>> definition of "more related". And the traditional systematists
>>> don't seem to have realized how biased it was against them.
>>
>> Let the Ranting of the Cladophobe commence!
>
> There never was any ranting by me on the subject, and there never
> will be.

More lies coming out of the King of Liar's mouth.

>
> "Cladophobe" is insincere because it implies an unwarranted
> fear of cladistic classification. I'm perfectly OK with it,
> and you know that.

You're perfectly okay with it because you are one? Just like
"Cladophile" is insincere because it implies an unwarranted obsession
withcladistics.

>
>
>> Seriously, your dismissal of
>> the term "more related" is especially idiotic in light of your support
>> for Linnaean taxonomy:
>
> Side by side with the only one YOU can stomach, let it not be forgot.
>
>> "No one would argue that Mitochondrial Eve is
>> more closely related to us than to her own mother." Come on, Peter, at
>> least be consistent with your bullshit.
>
> I am perfectly consistent, and if you can't see that, you need
> to see a psychiatrist.

Psychological projection noted.

>
> But I think you do see that, and are thus being completely
> insincere about accusing me of inconsistency.

Psychological projection noted.

>
>>>
>>> I've been through an argument about that bizarre (when compared to the
>>> everyday meaning of "more related") definition with Oxyaena.
>
> And the Mitochondrial Eve analogy is designed to show just
> HOW bizarre it is. That's consistency, you insufferable troll.
>
>
>>> That neither you nor John saw fit to enter into that argument
>>> is your loss, not mine. The upshot is that John started a new
>>> thread that doesn't even hint at this argument.
>>
>> You're an idiot.
>
> I think I see why you broke your "promise" so soon: you could make this
> illogical insult without what I wrote having been a "bygone".

Consider the numerous times you've insulted me over the past few months,
and this statement is hollow immediately upon being typed into the keyboard.

>
>
>> I have no interest in repeating myself to you over why
>> cladistics is a better system at representing evolutionary relationships
>> than Linnaean taxonomy is.
>
> It's nice to see that even you have limits where broken record routines
> are concerned. I'm referring to endless repetitions
> of "better showing of relationships" with no attempt to address
> the revolutionary nature of the cladophile way with the word
> "relationships."

I`m not going to waste my time.

>
> By the way, you DO realize that you DID repeat yourself, don't you?
> But perhaps this is the last time, yes?

I have no need to repeat myself, as I've made perfectly clear.

>
>
>> HAND
>
> The same to you, with the (probably forlorn) hope that you will
> make good on the message implied by your "forgery" of what I wrote.

If you think it's a forgery then perhaps you should read what you write.

[Peter Nyikos]

You are describing yourself, not me. And now I will let you know how.

I documented your most over-the-top slander in "Pterosaur dietary
hypotheses," and you snipped it in reply, not daring to confront it.
It went:

In short, another demonstration of your
dishonesty, blatant distorting of the facts, and outright slander.
I could sue you for libel, Peter, but unlike you I`m a decent person so
I won't.

What you called a "slander" and legally actionable "libel" was a
COMPLETELY accurate statement:

you *also* showed your ignorance about when life
could reasonably be expected to arise and evolve in our universe.

And, after your mangling of the concept of "slander" and "libel,"
I showed you just how accurate that statement of mine was.
You had written the following benighted, ignorant comment:

Considering that the universe is only 13.8 billion years old, and the
universe only settled down enough for life to develop some 4.5 Ga, ala
when our Solar System formed, this makes sense.

I gave you a carefully reasoned analysis of why this is completely false,
ending in:

the planetary system within 100 light years of us
that SETI considered the best target for a long time
is Delta Pavonis, a G star like our sun. It is estimated to be
over 6.5 billion years old, yet has a higher percentage of
heavy elements than our sun.

https://en.wikipedia.org/wiki/Delta_Pavonis

I have documented all this, both in talk.origins and in
sci.bio.paleontology. Here is the data on the talk.origins post:

https://groups.google.com/d/msg/talk.origins/Xub9hqEyM0A/l7gpBG1zCAAJ
Subject: Re: The evolution of the bacterial flagellum: For Peter
Date: Fri, 27 Jul 2018 10:08:39 -0700 (PDT)
Message-ID: <8174902f-492c-4d99...@googlegroups.com>

The only reply anyone has made to the above post was you,
digging yourself in deeper with a two-line reply:

[snip mindless bullshit]

Fixed it for you, Petey.


And here is the data for the s.b.p. post.

https://groups.google.com/forum/#!original/sci.bio.paleontology/RNINuDOndSM/n9Iq_m2OBQAJ
Date: Fri, 3 Aug 2018 15:15:24 -0700 (PDT)
Message-ID: <9d03402c-db16-46c4...@googlegroups.com>
Subject: Re: Pterosaur dietary hypotheses

>
> >
> > I`m not going to dignify your bullshit
> > anymore by responding to you, consider this my last response to you,
> > Peter, period.
> >
> >>
> >>> "Jump on the bandwagon, or be left in the dustbin of history"
> >>> is not a valid argument for the real claim the three of you are making.
> >
> > And I see no sign of anyone here giving any other argument
> > against the stand I took below:
> >
> >>> The real claim is exemplified by what the Subject line should have been:
> >>>
> >>> Subject: Prohibition of paraphyly vs toleration thereof
> >>>
> >>> ... in what has replaced a classification where the overwhelming
> >>> majority of taxa were hypothesized as monophylic, even in the days of Romer.
> >>>
> >>> That classification has been consigned to the dustbin of history without
> >>> a fair hearing. The "cow - lungfish - trout" brouhaha that seems
> >>> to have been the decisive battle in the war that resulted in the
> >>> banishment of paraphyletic taxa was conducted with a cladophile-serving
> >>> definition of "more related". And the traditional systematists
> >>> don't seem to have realized how biased it was against them.
> >>
> >> Let the Ranting of the Cladophobe commence!
> >
> > There never was any ranting by me on the subject, and there never
> > will be.
>
> More lies coming out of the King of Liar's mouth.

This isn't talk.origins, Oxyaena. Casanova and jillery aren't
here to back you up on slanders like the above, nor is Martin
Harran here to commiserate with you. They did all that and more,
AFTER I posted the documentation you see above.

You've been spoiled rotten in talk.origins, and you don't seem
to realize that this is a totally different venue.

As the song in "Prince of Egypt" goes: "You're playing with the
big boys now."

>
> >
> > "Cladophobe" is insincere because it implies an unwarranted
> > fear of cladistic classification. I'm perfectly OK with it,
> > and you know that.
>
> You're perfectly okay with it because you are one?

I am not a cladistic classification, ninny. Can't you even READ?

> Just like
> "Cladophile" is insincere because it implies an unwarranted obsession
> with cladistics.

No it does not. It implies a love of phylogenetic trees, to the
exclusion of evolutionary trees. The former put all organisms,
extinct or extant, at the tips of their twigs. The latter put
as many organisms at nodes as the evidence warrants, showing
e.g. Merychippus to be ancestral to Equus.

Cladophiles want to banish evolutionary trees from science.
That is not an insult, that is something all of you are PROUD
of, because, as you put it, phylogenetic trees show "relationships"
more better than evolutionary trees do.

So don't lie that there is no such thing as cladophilia. Your
objections to the word are purely emotional.

>
> >
> >
> >> Seriously, your dismissal of
> >> the term "more related" is especially idiotic in light of your support
> >> for Linnaean taxonomy:
> >
> > Side by side with the only one YOU can stomach, let it not be forgot.
> >
> >> "No one would argue that Mitochondrial Eve is
> >> more closely related to us than to her own mother." Come on, Peter, at
> >> least be consistent with your bullshit.
> >
> > I am perfectly consistent, and if you can't see that, you need
> > to see a psychiatrist.
>
> Psychological projection noted.

Maybe I should be even more blunt. Your adopted Mama jillery isn't
here to bail you out of illogical lies like the above, nor is
your adopted Papa Casanova here to spin-doctor them into pearls of wisdom.

>
> >
> > But I think you do see that, and are thus being completely
> > insincere about accusing me of inconsistency.
>
> Psychological projection noted.

Nor is your admirer Martin Harran here to kiss it where it hurts,
you poor baby.

> >
> >>>
> >>> I've been through an argument about that bizarre (when compared to the
> >>> everyday meaning of "more related") definition with Oxyaena.
> >
> > And the Mitochondrial Eve analogy is designed to show just
> > HOW bizarre it is. That's consistency, you insufferable troll.

Why didn't you repeat your illogical lie here, where I showed it
to be illogical?


Remainder snipped, because I don't feel like indulging too much
in overkill.

Besides, I've already risked another patented John Harshman
"even-handed" "value-free" intrusion, "Stop bickering, children,"
or words to that effect.


Peter Nyikos

[Oxyaena]

On 8/8/2018 9:35 PM, Peter Nyikos wrote:
[snip personal attacks, snip baseless insults, snip libel, snip mindless
bullshit]

You're going into my killfile, now, bye!

[Peter Nyikos]

On Thursday, August 9, 2018 at 11:47:19 AM UTC-4, Oxyaena wrote:
> On 8/8/2018 9:35 PM, Peter Nyikos wrote:
> [snip personal attacks, snip baseless insults, snip libel, snip mindless
> bullshit]

All of them were by you, Thrinaxodon.

> You're going into my killfile, now, bye!

Thank you for flinging me into the briar patch.

Did you know that Br'er Rabbit's "Christian" name was Peter? :-) :-)


Peter Nyikos


PS I'm still addressing you because I suspect my stay in the killfile
will be no longer than my stay in the "no-response" file was
after you wrote,

"consider this my last response to you,
Peter, period."

--quoted in my second Aug 8 reply to you on this thread.

[Peter Nyikos]

On Wednesday, August 8, 2018 at 11:27:00 AM UTC-4, John Harshman wrote:
> On 8/8/18 6:28 AM, Peter Nyikos wrote:
> > On Tuesday, August 7, 2018 at 11:13:50 PM UTC-4, John Harshman wrote:
> >> On 8/7/18 5:42 PM, Peter Nyikos wrote:
> >>> On Wednesday, August 1, 2018 at 11:28:36 PM UTC-4, John Harshman wrote:
> >>>> Rather than clog up a thread on pterosaurs, let's argue about the
> >>>> benefits of paraphyly vs. monophyly here. There are several
> >>>> distinguishable issues:
> >>>>
> >>>> 1. Can paraphyletic groups be more useful in classification than strict
> >>>> adherence to monophyly?
> >>>
> >>> Poorly worded. Ever since 2002 all I have ever argued for was for
> >>> cladophiles like you not to ban paraphyletic groups, but to admit
> >>> them side by side with monophyletic ones, because they also
> >>> contribute to our understanding of evolution.
> >>
> >> It isn't quite clear what "side by side" means.
> >
> > It ought to be clear. I've explained it at least once a year, on the
> > average, since 2010. Evidently all those comparisons with the
> > side by side Dewey Decimal System and the Library of Congress system
> > "went in one ear and out the other," as my grade school and high school
> > teachers put it. [This was in the days before "middle school" became
> > a widespread institution.]
>
> You are being very uncommunicative lately.

I am much more communicative than you in at least one respect:
I am usually proactive, volunteering all kinds of on-topic information
(including data) and reasoned arguments.

You are overwhelmingly reactive, not proactive. You are like a boxer who is
a counterpuncher, almost always waiting until the opponent (or sparring
partner) throws a punch or initiates a combination, hoping to exploit
weaknesses in the other's movements.


<snip lots of text, to be dealt with in separate posts, leaving in only:>

> >>>> 2. Should particular fossil "species" be declared to be ancestors or
> >>>> ancestor candidates, and if so, what is gained?

[...]

> >>>> 3. Is it useful to declare higher taxa ancestral to other taxa?

[...]

> >>>> 4. Are "evolutionary trees" (in which taxa are ancestral, either by
> >>>> placing species at internal nodes or by having taxa emerge from
> >>>> "bubbles") ever more useful than phylogenetic trees (i.e. cladograms
> >>>> with or without meaningful branch lengths)?
> >>>> Discuss. My answers of course would be no, no, no, and no.

[...]

> >>> And I don't mean emotional arguments like the following, which
> >>> only lends support to the thesis that your negative answers
> >>> are ideologically and not scientifically based.

> >>> I didn't read all the way through, since the cladophobe bullshit
> >>> infested every corner of my screen I quickly clicked out of it lest I
> >>> get your disease.
https://groups.google.com/d/msg/sci.bio.paleontology/RNINuDOndSM/cy3gGiLiBQAJ
>>

> >> How does this lend support to any thesis about me?

Not about YOU, but about your four "no" answers, all of which
exemplify cladophilia. I explained the concept yesterday
to Oxyaena:

It implies a love of phylogenetic trees, to the
exclusion of evolutionary trees. The former put all organisms,
extinct or extant, at the tips of their twigs. The latter put
as many organisms at nodes as the evidence warrants, showing
e.g. Merychippus to be ancestral to Equus.

Cladophiles want to banish evolutionary trees from science.
That is not an insult, that is something all of you are PROUD
of, because, as you put it, phylogenetic trees show "relationships"

better than evolutionary trees do.

> >> I didn't say that.
> >> That would appear to be Oxyaena.
> >
> > It was. And you show no sign of disapproval.
>
> I tend not to respond to empty trash talk, either by you or others.

"trash talk" = personal criticism. Oxyaena called criticisms of
cladophilia a "disease". That is not personal, even though a lot
of the rest of Oxyaena's comment was.

> > As I was hinting above, it takes two to tango.
>
> No idea what that means. Perhaps you should do more than hint.

I mean, you are being uncommunicative about your attitude towards
what Oxyaena wrote. For all I know, this could just be a matter
of personal preferences, like Oxyaena suggesting Eight O'Clock coffee
when you prefer Starbucks.

> >>> I had written:
> >>> By the way, you haven't responded to my post of yesterday
> >>> in reply to Ruben Safir, even though there was actual
> >>> paleontology at the end, not just systematics. Can you say "double
> >>> standard"?
> >>> --- from the Pterosaur thread to which you refer at the beginning
> >>>
> >>> And the response was what you are reading above.
> >>
> >> Not my response, though.

No hint of what your response might be, though. You are 0% proactive here.

> > What is YOUR excuse for not entering into my argument with Ruben?
>
> I don't need an excuse. I enter when I have something interesting to say
> or am interested in getting an answer.

That might explain why you aren't elaborating on
"no, no, no, and no" even now.

> Since I don't recall what your
> argument with Ruben is, I probably had neither reason. You should not
> take that an an affront.

After seeing our exchange again, you might see its relevance to this thread.
However, it was the follow-up two posts later that is most relevant to this
"Paraphyly vs. Monophyly" thread:

________________________ repost _________________

On Wednesday, August 1, 2018 at 1:16:36 PM UTC-4, ruben safir wrote:
> On 07/31/2018 08:47 AM, Peter Nyikos wrote:
> > "a non-avian, non-mammalian amniote."
>
> ROFL!
>
> It is interesting that an entire family that we all felt secure we
> understood, Reptiles, ended up a non-existing phylogetic group.

You are well over a century behind the times, Ruben. A century ago,
no paleontologist worth his salt was ignorant of the fact that
mammals and birds descended from what was universally understood
to be the class Reptilia.

But I don't think ANY paleontologist lost any sleep over the fact
that he was dealing in what is NOW called a "paraphyletic taxon."
I've often posted to s.b.p. about how Romer, near the beginning
of his classic _Vertebrate Paleontolgy_ (1945 edition) talked
about "horizontal" and "vertical" subdivisions of a phylogenetic
tree, and gave pros [1] and cons of each method.

The "horizontal" explicitly produced paraphyletic taxa, [2] the
"vertical" just as explicitly produced clades -- the only things
that Harshman and Oxyaena (and, if she is telling the truth, her husband)
will ever call "taxa".

Over a century of systematics (when nobody thought there was
anything the matter with horizontal subdivisions that produced
paraphyletic taxa) shoved down the memory hole.

[1] I'll gladly expound on the pros of the traditional classification,
if you are willing to listen.

[2] It has to be done the way Romer illustrated it, to avoid
polyphyletic taxa. Those were pretty well purged from the formal
classification, with the exception of Holostei, whose polyphyletic
nature was explicitly acknowledged by Romer [yes, he used the
word "polyphyletic"].



> There
> are no reptiles. We have Archosaurs, Squamata, Synapsida, Mammals,
> Aves, Dinasoria, Testudinata..

Your use of lower case "reptiles" makes this a fallacious pastiche of formal
and everyday usage.


> Turles, Snakes and Crocs are less related to each other than Birds and
> Crocs..
>
> What an amazing discovery.

Done, and taken in its stride, before any of us was born.

You have a lot of catching up to do. :-)

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina

http://people.math.sc.edu/nyikos/

PS You snipped the part about Palaeospondylus. THAT was paleontology,
as opposed to systematics, and I was hoping it would interest
you on that account.

=============================== end of repost ================= from
https://groups.google.com/d/msg/sci.bio.paleontology/RNINuDOndSM/nur467zqBQAJ
Date: Wed, 1 Aug 2018 13:09:44 -0700 (PDT)
Message-ID: <efab5ce1-9b1d-4dad...@googlegroups.com>

Subject: Re: Pterosaur dietary hypotheses

Discuss. I'll be content even with a 100% reactive reply.


Peter Nyikos

[John Harshman]

Changing the subject to my behavior is not really relevant to whether
you're uncommunicative.

>>>>>> 2. Should particular fossil "species" be declared to be ancestors or
>>>>>> ancestor candidates, and if so, what is gained?
> [...]
>>>>>> 3. Is it useful to declare higher taxa ancestral to other taxa?
> [...]
>>>>>> 4. Are "evolutionary trees" (in which taxa are ancestral, either by
>>>>>> placing species at internal nodes or by having taxa emerge from
>>>>>> "bubbles") ever more useful than phylogenetic trees (i.e. cladograms
>>>>>> with or without meaningful branch lengths)?
>>>>>> Discuss. My answers of course would be no, no, no, and no.
>
> [...]
>
>>>>> And I don't mean emotional arguments like the following, which
>>>>> only lends support to the thesis that your negative answers
>>>>> are ideologically and not scientifically based.
>
>>>>> I didn't read all the way through, since the cladophobe bullshit
>>>>> infested every corner of my screen I quickly clicked out of it lest I
>>>>> get your disease.
> https://groups.google.com/d/msg/sci.bio.paleontology/RNINuDOndSM/cy3gGiLiBQAJ
>>>
>
>>>> How does this lend support to any thesis about me?
>
> Not about YOU, but about your four "no" answers, all of which
> exemplify cladophilia.

Then why did quote something else entirely?

> I explained the concept yesterday
> to Oxyaena:
>
> It implies a love of phylogenetic trees, to the
> exclusion of evolutionary trees. The former put all organisms,
> extinct or extant, at the tips of their twigs. The latter put
> as many organisms at nodes as the evidence warrants, showing
> e.g. Merychippus to be ancestral to Equus.
>
> Cladophiles want to banish evolutionary trees from science.
> That is not an insult, that is something all of you are PROUD
> of, because, as you put it, phylogenetic trees show "relationships"
> better than evolutionary trees do.

I will note that "evolutionary tree" is a bit of propagandistic claiming
of the high ground, identical to Mayr's "evolutionary taxonomy".
Phylogenetic trees are explicitly evolutionary, just as much as
"evolutionary" trees are.

Yes, cladophiles (by which we mean almost everyone living who does
anything involving phylogeny, and which is also a coinage for propaganda
purposes) want to banish bubble diagrams from science. There are good
reasons: bubble diagrams are much less clear about their claims than
phylogenetic trees are. Lack of clarity is not a virtue.

>>>> I didn't say that.
>>>> That would appear to be Oxyaena.
>>>
>>> It was. And you show no sign of disapproval.
>>
>> I tend not to respond to empty trash talk, either by you or others.
>
> "trash talk" = personal criticism. Oxyaena called criticisms of
> cladophilia a "disease". That is not personal, even though a lot
> of the rest of Oxyaena's comment was.

I tend not to respond to anything embedded in trash talk either. So I
tend not to read stuff Oxyaena says to you.

>>> As I was hinting above, it takes two to tango.
>>
>> No idea what that means. Perhaps you should do more than hint.
>
> I mean, you are being uncommunicative about your attitude towards
> what Oxyaena wrote. For all I know, this could just be a matter
> of personal preferences, like Oxyaena suggesting Eight O'Clock coffee
> when you prefer Starbucks.

My attitude is that I don't like to read what Oxyaena says to you and
often do not.

Can we get back to paleontology?

>>>>> I had written:
>>>>> By the way, you haven't responded to my post of yesterday
>>>>> in reply to Ruben Safir, even though there was actual
>>>>> paleontology at the end, not just systematics. Can you say "double
>>>>> standard"?
>>>>> --- from the Pterosaur thread to which you refer at the beginning
>>>>>
>>>>> And the response was what you are reading above.
>>>>
>>>> Not my response, though.
>
> No hint of what your response might be, though. You are 0% proactive here.

I don't even know what post you're talking about. What thread was it in?

>>> What is YOUR excuse for not entering into my argument with Ruben?
>>
>> I don't need an excuse. I enter when I have something interesting to say
>> or am interested in getting an answer.
>
> That might explain why you aren't elaborating on
> "no, no, no, and no" even now.

The point of the OP was to get you to provide reasons for yes, yes, yes,
and yes, because I'm not clear on what they would be.

Go for it.

> [2] It has to be done the way Romer illustrated it, to avoid
> polyphyletic taxa. Those were pretty well purged from the formal
> classification, with the exception of Holostei, whose polyphyletic
> nature was explicitly acknowledged by Romer [yes, he used the
> word "polyphyletic"].

I don't have the 1945 edition, just 1966. Are these illustrations the same?

>> There
>> are no reptiles. We have Archosaurs, Squamata, Synapsida, Mammals,
>> Aves, Dinasoria, Testudinata..
>
> Your use of lower case "reptiles" makes this a fallacious pastiche of formal
> and everyday usage.
>
>
>> Turles, Snakes and Crocs are less related to each other than Birds and
>> Crocs..
>>
>> What an amazing discovery.
>
> Done, and taken in its stride, before any of us was born.
>
> You have a lot of catching up to do. :-)

It seems to me that you are underestimating how long it's been known
that "Reptilia" is paraphyletic. Certainly that was T. H. Huxley's view
in the 1860s.

What other sort of response were you looking for? I don't really see
anything to talk about. Ruben was confused, you set him straight, and in
the process you alluded to an argument you might make for paraphyletic
taxa. Nothing much to talk about until you actually make that argument.

[erik simpson]

Discuss what, exactly? Your "arguments" with Oxyaena? I'll pass on that. Your
chastisement of Ruben? Likewise. Your high regard for a 78-year old reference?
We've been there and done that. Paleospondylyus? Where did you talk about
that? An interesting fossil (note sigularity of same). Enigmatic, as they say.
Or do you want to talk about your ideas of phylogeny? If so, are there any
changes in your thinking over your yearly recap?

[Oxyaena]

On 8/9/2018 3:07 PM, Peter Nyikos wrote:
> On Thursday, August 9, 2018 at 11:47:19 AM UTC-4, Oxyaena wrote:
>> On 8/8/2018 9:35 PM, Peter Nyikos wrote:
>> [snip personal attacks, snip baseless insults, snip libel, snip mindless
>> bullshit]
>
> All of them were by you, Thrinaxodon.

Lack of self reflection, psychological projection, and blatant
dishonesty noted, Nyikos.

>
>
>> You're going into my killfile, now, bye!
>
> Thank you for flinging me into the briar patch.
>
> Did you know that Br'er Rabbit's "Christian" name was Peter? :-) :-)
>

Do you have a point to make, or are you merely pontificating for the
point of pontificating?

>
> Peter Nyikos
>
>
> PS I'm still addressing you because I suspect my stay in the killfile
> will be no longer than my stay in the "no-response" file was
> after you wrote,

My computer doesn't save any of my user information each time I log out
or shut it down, so I stay on as long as I can before I have to shut it
down since none of the data after a certain point is saved, so what's
the point in killfiling you if it won't stick. My tolerance for your
shenanigans ranges from day to day, varying from amusement at your
hypocrisy and lack of self-reflection to rage at the pure bullshit you
write about me on a daily basis.

>
> "consider this my last response to you,
> Peter, period."
> --quoted in my second Aug 8 reply to you on this thread.
>

See above.

[Oxyaena]

Lack of self-reflection noted. Look up the difference between "slander"
and "libel", then respond back. And nothing I've written about you
classifies as slanderous, unlike the horseshit you fling out about me on
a daily basis.



>

> I documented your most over-the-top slander in "Pterosaur dietary
> hypotheses," and you snipped it in reply, not daring to confront it.
> It went:

You're only digging yourself deeper, Nyikos.

>
> In short, another demonstration of your
> dishonesty, blatant distorting of the facts, and outright slander.
> I could sue you for libel, Peter, but unlike you I`m a decent person so
> I won't.
>
> What you called a "slander" and legally actionable "libel" was a
> COMPLETELY accurate statement:

You've never demonstrated it to be so, as Casanova pointed out to you in
t.o. on a thread you ran away from.

>
> you *also* showed your ignorance about when life
> could reasonably be expected to arise and evolve in our universe.

Another baseless assertion. You must love proving me right, you do it so
often.

>
> And, after your mangling of the concept of "slander" and "libel,"
> I showed you just how accurate that statement of mine was.
> You had written the following benighted, ignorant comment:

You're describing yourself, not me.

>
> Considering that the universe is only 13.8 billion years old, and the
> universe only settled down enough for life to develop some 4.5 Ga, ala
> when our Solar System formed, this makes sense.

There was nothing "ignorant" about it, until a few billion years ago the
universe was a violent, chaotic place, and the formation of planets
during that time only proves planets were capable of forming, not life.

>
> I gave you a carefully reasoned analysis of why this is completely false,
> ending in:

I presume "carefully reasoned analysis" actually means "hastily written
claptrap", in order to comprehend your language one requires a key of
the euphemisms you use and their actual meanings.

>
> the planetary system within 100 light years of us
> that SETI considered the best target for a long time
> is Delta Pavonis, a G star like our sun. It is estimated to be
> over 6.5 billion years old, yet has a higher percentage of
> heavy elements than our sun.
>
> https://en.wikipedia.org/wiki/Delta_Pavonis
>
> I have documented all this, both in talk.origins and in
> sci.bio.paleontology. Here is the data on the talk.origins post:

Your "documentations" aren't worth shit.

So? Refuting bullshit is the same everywhere, regardless of where it is.

>
> You've been spoiled rotten in talk.origins, and you don't seem
> to realize that this is a totally different venue.

You're an idiot, and a hypocrite as well, since you insult me here yet
you hypocritically accuse me of being an "insult addict". Does the term
"self-reflection" mean anything to you, Narcissus?

>
> As the song in "Prince of Egypt" goes: "You're playing with the
> big boys now."
>
>>
>>>
>>> "Cladophobe" is insincere because it implies an unwarranted
>>> fear of cladistic classification. I'm perfectly OK with it,
>>> and you know that.
>>
>> You're perfectly okay with it because you are one?
>
> I am not a cladistic classification, ninny. Can't you even READ?

Unlike you, yes, I can read. BTW, I was calling you a cladophobe, not a
cladistic classification.

>
>
>> Just like
>> "Cladophile" is insincere because it implies an unwarranted obsession
>> with cladistics.
>
> No it does not. It implies a love of phylogenetic trees, to the
> exclusion of evolutionary trees. The former put all organisms,
> extinct or extant, at the tips of their twigs. The latter put
> as many organisms at nodes as the evidence warrants, showing
> e.g. Merychippus to be ancestral to Equus.

So, in other words, double standards?

>
> Cladophiles want to banish evolutionary trees from science.
> That is not an insult, that is something all of you are PROUD
> of, because, as you put it, phylogenetic trees show "relationships"
> more better than evolutionary trees do.

So, in other words, you're concocting up some bogus rationalization for
the insincere slur you invented? I`m not surprised, you *love* playing
word games to get out of tight spaces.

>
> So don't lie that there is no such thing as cladophilia. Your
> objections to the word are purely emotional.

Dishonesty and insult duly noted.

>
>>
>>>
>>>
>>>> Seriously, your dismissal of
>>>> the term "more related" is especially idiotic in light of your support
>>>> for Linnaean taxonomy:
>>>
>>> Side by side with the only one YOU can stomach, let it not be forgot.
>>>
>>>> "No one would argue that Mitochondrial Eve is
>>>> more closely related to us than to her own mother." Come on, Peter, at
>>>> least be consistent with your bullshit.
>>>
>>> I am perfectly consistent, and if you can't see that, you need
>>> to see a psychiatrist.
>>
>> Psychological projection noted.
>
> Maybe I should be even more blunt. Your adopted Mama jillery isn't
> here to bail you out of illogical lies like the above, nor is
> your adopted Papa Casanova here to spin-doctor them into pearls of wisdom.

Baseless insults noted.

>
>>
>>>
>>> But I think you do see that, and are thus being completely
>>> insincere about accusing me of inconsistency.
>>
>> Psychological projection noted.
>
> Nor is your admirer Martin Harran here to kiss it where it hurts,
> you poor baby.

Baseless insult noted.

>
>>>
>>>>>
>>>>> I've been through an argument about that bizarre (when compared to the
>>>>> everyday meaning of "more related") definition with Oxyaena.
>>>
>>> And the Mitochondrial Eve analogy is designed to show just
>>> HOW bizarre it is. That's consistency, you insufferable troll.
>
> Why didn't you repeat your illogical lie here, where I showed it
> to be illogical?

Bullshit noted.

>
>
> Remainder snipped, because I don't feel like indulging too much
> in overkill.

Of course, you don't like dealing with things that inconvenience, like
90% of every post I've ever written to you. You usually snip it, saying
you'll "deal with it tomorrow", and tomorrow never comes. I can't count
the number of times you've said that and didn't come through with that
statement.

>
> Besides, I've already risked another patented John Harshman
> "even-handed" "value-free" intrusion, "Stop bickering, children,"
> or words to that effect.

You've more than risked it.

>
>
> Peter Nyikos
>

[Peter Nyikos]

On Thursday, August 9, 2018 at 5:32:08 PM UTC-4, John Harshman wrote:
> On 8/9/18 1:26 PM, Peter Nyikos wrote:

> > I explained the concept [of cladophilia] yesterday

> > to Oxyaena:
> >
> > It implies a love of phylogenetic trees, to the
> > exclusion of evolutionary trees. The former put all organisms,
> > extinct or extant, at the tips of their twigs. The latter put
> > as many organisms at nodes as the evidence warrants, showing
> > e.g. Merychippus to be ancestral to Equus.
> >
> > Cladophiles want to banish evolutionary trees from science.
> > That is not an insult, that is something all of you are PROUD
> > of, because, as you put it, phylogenetic trees show "relationships"
> > better than evolutionary trees do.
>
> I will note that "evolutionary tree" is a bit of propagandistic claiming
> of the high ground,

Au contraire, it is an effort to claim back SOME ground from the
way cladophiles co-opted the words "phylogenetic" and "relationship"
to refer to concepts that were once used to refer to direct
ancestor-descendant relationships and degree of proximity in morphology
[with every effort to distinguish between homology and convergence]
IN ADDITION TO the things that they now denote.

It is the same way with "monophyly". Because systematists once were
perfectly accepting of what Hennig coined the word "paraphyletic" for,
they applied "monophyletic" indiscriminately to both kinds of groups.

It was to fight this co-optation of "monophyletic" that Ashlock
coined the word "holophyletic". These last two days, for the
first time, I read what Carroll wrote in his huge _Vertebrate Paleontology
and Evolution_ (1988) on pp. 5-6 and 11-13 and was amazed, on the one
hand, to see how he meekly went along with the cladophile-friendly version
of the term "relationship" and, on the other hand, how critical he was
of the cladophile ban on paraphyletic groups and how persistently
he used "holophyletic" in an effort to preserve the original meaning
of "monophyletic."

It's been claimed that Carroll has gone over to the side of the
cladists, but was this "going over" anything more than abandoning
"holphyletic" in the realization that he was just beating his head
against stone walls?

> identical to Mayr's "evolutionary taxonomy".

Did cladophiles also co-opt the word "phylogenetic" to describe
their taxonomy, and eschew calling it "cladistic taxonomy"?
Or is "objective taxonomy" their term of choice for the only
taxonomy they tolerate?

> Phylogenetic trees are explicitly evolutionary, just as much as
> "evolutionary" trees are.

Exactly the opposite is true. Phylogenetic trees hide all evidence of
ancestor-descendant relationships. Deliberately so, in the case
of cladophiles.


Several times, I have made the analogy that one could also have
a "cladogram" of mountains, using characters involving geological
concepts. And one could easily apply the word "evolution" to what
is now called "orogeny".

>
> Yes, cladophiles (by which we mean almost everyone living who does
> anything involving phylogeny,

"we" is inappropriate since you have consistently fought
against the word "cladophile", though not as emotionally
as Oxyaena. You should have written "cladistic systematists,"
which simply implies using cladistic systematics to build evolutionary
trees, without any publicly expressed desire to ban all other
classification systems.

> and which is also a coinage for propaganda
> purposes)

Co-optation, not coinage. "Ontogeny recapitulates phylogeny" is a term
that predates Hennigian systematics and perhaps even Hennig himself.

> want to banish bubble diagrams from science. There are good
> reasons: bubble diagrams are much less clear about their claims than
> phylogenetic trees are.

Their claims do not go beyond what their illustrators
believe the evidence clearly shows. That is a virtue
which you seem to think is a vice:

> Lack of clarity is not a virtue.

++++++++++++++++++++++++++++++++ sarcasm on

Yes, let's have clarity, as exemplified by the following
passage from Carroll's 1988 book (p.6):

The suborder Pinnipedia was long used to refer to both
seals (Phocoidea) and the sea lions and walruses (Otaroidea).
We now recognize that each group evolved independently
from separate families of terrestrial carnivores, rather
than evolving from a single common ancestor.

Now, of course, we have clarity in the opposite direction, returning
to the old "clarity" which made Pinnipedia monophyletic.

+++++++++++++++++++++++++++++++++++ sarcasm off

And is the present "consensus" really correct, the way the
1988 "consensus" does not seem to have been? Might not the
pendulum swing in the opposite direction again?

Last Friday, I went with a daughter to the excellent Riverbanks Zoo.
At one point our itinerary took us to the seal/sea lion exhibit.
We noticed how a seal that kept circling close to us used its
hind flippers as though they were fins -- in a sideways motion like
those of sharks and ichthyosaurs and the otter shrew. The sea
lions, on the other hand, used an up and down motion like those
of cetaceans and beavers.

Does "morpological" behavior, like this, ever enter into cladograms?


Peter Nyikos
Professor, Department of Mathematics -- standard disclaimer--

[John Harshman]

On 8/13/18 4:44 AM, Peter Nyikos wrote:
> On Thursday, August 9, 2018 at 5:32:08 PM UTC-4, John Harshman wrote:
>> On 8/9/18 1:26 PM, Peter Nyikos wrote:
>
>>> I explained the concept [of cladophilia] yesterday
>>> to Oxyaena:
>>>
>>> It implies a love of phylogenetic trees, to the
>>> exclusion of evolutionary trees. The former put all organisms,
>>> extinct or extant, at the tips of their twigs. The latter put
>>> as many organisms at nodes as the evidence warrants, showing
>>> e.g. Merychippus to be ancestral to Equus.
>>>
>>> Cladophiles want to banish evolutionary trees from science.
>>> That is not an insult, that is something all of you are PROUD
>>> of, because, as you put it, phylogenetic trees show "relationships"
>>> better than evolutionary trees do.
>>
>> I will note that "evolutionary tree" is a bit of propagandistic claiming
>> of the high ground,
>
> Au contraire, it is an effort to claim back SOME ground from the
> way cladophiles co-opted the words "phylogenetic" and "relationship"
> to refer to concepts that were once used to refer to direct
> ancestor-descendant relationships and degree of proximity in morphology
> [with every effort to distinguish between homology and convergence]
> IN ADDITION TO the things that they now denote.

Tomato, tomahto.

> It is the same way with "monophyly". Because systematists once were
> perfectly accepting of what Hennig coined the word "paraphyletic" for,
> they applied "monophyletic" indiscriminately to both kinds of groups.
>
> It was to fight this co-optation of "monophyletic" that Ashlock
> coined the word "holophyletic". These last two days, for the
> first time, I read what Carroll wrote in his huge _Vertebrate Paleontology
> and Evolution_ (1988) on pp. 5-6 and 11-13 and was amazed, on the one
> hand, to see how he meekly went along with the cladophile-friendly version
> of the term "relationship" and, on the other hand, how critical he was
> of the cladophile ban on paraphyletic groups and how persistently
> he used "holophyletic" in an effort to preserve the original meaning
> of "monophyletic."
>
> It's been claimed that Carroll has gone over to the side of the
> cladists, but was this "going over" anything more than abandoning
> "holphyletic" in the realization that he was just beating his head
> against stone walls?

You would have to read his subsequent book, which I have not.

>> identical to Mayr's "evolutionary taxonomy".
>
> Did cladophiles also co-opt the word "phylogenetic" to describe
> their taxonomy, and eschew calling it "cladistic taxonomy"?
> Or is "objective taxonomy" their term of choice for the only
> taxonomy they tolerate?

It's "phylogenetic" sometimes, but usually "cladistic".

>> Phylogenetic trees are explicitly evolutionary, just as much as
>> "evolutionary" trees are.
>
> Exactly the opposite is true. Phylogenetic trees hide all evidence of
> ancestor-descendant relationships. Deliberately so, in the case
> of cladophiles.

No, they hide no evidence. They reflect what evidence we actually have
rather than fabricating relationships we don't know (as in assignment of
species to internal nodes) or potentially hiding relationships we do (as
in amorphous bubble diagrams). Now of course the hypothetical internal
nodes are just as much a claim of evolution as the known species you
want to put there.

> Several times, I have made the analogy that one could also have
> a "cladogram" of mountains, using characters involving geological
> concepts. And one could easily apply the word "evolution" to what
> is now called "orogeny".

You have made that claim, but you have never even tried to back it up.
You could not have a cladogram of mountains as anything more than an
artificial construct that reflects no underlying reality. In
phylogenetics, on the other hand, common descent is that underlying reality.

>> Yes, cladophiles (by which we mean almost everyone living who does
>> anything involving phylogeny,
>
> "we" is inappropriate since you have consistently fought
> against the word "cladophile", though not as emotionally
> as Oxyaena. You should have written "cladistic systematists,"
> which simply implies using cladistic systematics to build evolutionary
> trees, without any publicly expressed desire to ban all other
> classification systems.

"Ban" is the wrong word, since nobody has such power. And that's what I
mean when I use he word; I was just pointing out that almost every
living systematist is a "cladophile".

>> and which is also a coinage for propaganda
>> purposes)
>
> Co-optation, not coinage. "Ontogeny recapitulates phylogeny" is a term
> that predates Hennigian systematics and perhaps even Hennig himself.

What does that have to do with "cladophile"?

>> want to banish bubble diagrams from science. There are good
>> reasons: bubble diagrams are much less clear about their claims than
>> phylogenetic trees are.
>
> Their claims do not go beyond what their illustrators
> believe the evidence clearly shows. That is a virtue
> which you seem to think is a vice:

It's unclear what a bubble diagram is intended to claim. A polytomy on a
phylogenetic tree would be much clearer.

>> Lack of clarity is not a virtue.
>
> ++++++++++++++++++++++++++++++++ sarcasm on
>
> Yes, let's have clarity, as exemplified by the following
> passage from Carroll's 1988 book (p.6):
>
> The suborder Pinnipedia was long used to refer to both
> seals (Phocoidea) and the sea lions and walruses (Otaroidea).
> We now recognize that each group evolved independently
> from separate families of terrestrial carnivores, rather
> than evolving from a single common ancestor.
>
> Now, of course, we have clarity in the opposite direction, returning
> to the old "clarity" which made Pinnipedia monophyletic.
>
> +++++++++++++++++++++++++++++++++++ sarcasm off
>
> And is the present "consensus" really correct, the way the
> 1988 "consensus" does not seem to have been? Might not the
> pendulum swing in the opposite direction again?

Yes, and no, for which you have to thank both modern methods of analysis
and the modern accessibility of molecular data. Anyway, you mistake
clarity of hypothesis for certainty of hypothesis. I'm talking about the
first and you attack the second. I would note that Carroll's book was
behind the times even in 1988, specifically because he made no use of
cladistic methods. Check out Benton for a corrective.

> Last Friday, I went with a daughter to the excellent Riverbanks Zoo.
> At one point our itinerary took us to the seal/sea lion exhibit.
> We noticed how a seal that kept circling close to us used its
> hind flippers as though they were fins -- in a sideways motion like
> those of sharks and ichthyosaurs and the otter shrew. The sea
> lions, on the other hand, used an up and down motion like those
> of cetaceans and beavers.
>
> Does "morpological" behavior, like this, ever enter into cladograms?

Not in such a crude form, but yes. Cladistic methods do not involve
ignoring data, as you seem to think.

I would be happier if you started presenting a case in favor of your
views on classification, ancestors, and such.

[Oxyaena]

,
>
> "we" is inappropriate since you have consistently fought
> against the word "cladophile", though not as emotionally
> as Oxyaena.

You deliberately lie about what I wrote to you as being merely
"emotional". What I actually wrote to you was this:

"> You may think it is flawed to think about relationships in any
> different way, but if so, I don't think you should discuss your
> family tree in everyday conversation. Especially not if there
> is a "long branch" leading to great-great grandchildren of a sibling of
> of yours, making them all more closely related to you than you
> are to your own grandparents.
>
>
>> something Linnaean taxonomy, with its emphasis on paraphyletic
>> solutions, wouldn't be able to do.
>
> It can however do a better job with relationships the way ordinary people
> discuss their relatives.

That's the whole reason why Linnaean taxonomy fails, because it doesn't
do a good job at explaining species-level or higher relationships
between taxa, only individuals. I am not on opposite sides here, Peter,
I too believe that modern taxonomy should be reformed or refined, with
less emphasis on ultra-cladistics, but I don't believe that Linnaean
taxonomy is the right way to do so."

Here's one of the many pieces of documentation that you request which
can be easily found by scrolling through a fucking thread. You're
probably going to ignore this, since it is contrary to the picture you
portray of me, as a raging berserker, but since when did honesty
actually matter to you, Nyikos?

[Peter Nyikos]

I both request and recommend that you cease and desist from using
the term "trash talk" until you give a very different definition
from the one I gave below ("personal criticism") because as it
stands, you are in the unenviable position of persisting in it up here.

> >>>>>> 2. Should particular fossil "species" be declared to be ancestors or
> >>>>>> ancestor candidates, and if so, what is gained?
> > [...]
> >>>>>> 3. Is it useful to declare higher taxa ancestral to other taxa?
> > [...]
> >>>>>> 4. Are "evolutionary trees" (in which taxa are ancestral, either by
> >>>>>> placing species at internal nodes or by having taxa emerge from
> >>>>>> "bubbles") ever more useful than phylogenetic trees (i.e. cladograms
> >>>>>> with or without meaningful branch lengths)?
> >>>>>> Discuss. My answers of course would be no, no, no, and no.
> >
> > [...]
> >
> >>>>> And I don't mean emotional arguments like the following, which
> >>>>> only lends support to the thesis that your negative answers
> >>>>> are ideologically and not scientifically based.
> >
> >>>>> I didn't read all the way through, since the cladophobe bullshit
> >>>>> infested every corner of my screen I quickly clicked out of it lest I
> >>>>> get your disease.
> > https://groups.google.com/d/msg/sci.bio.paleontology/RNINuDOndSM/cy3gGiLiBQAJ
> >>>
> >
> >>>> How does this lend support to any thesis about me?
> >
> > Not about YOU, but about your four "no" answers, all of which
> > exemplify cladophilia.
>
> Then why did quote something else entirely?

It is NOT something else. It is an illustrative example of the
lengths to which cladophilia takes some people. But you seem
reluctant to agree that it expresses an emotional, ideological
opposition rather than a reasoned one.


Here, I deleted some text on which I expounded at length
this morning.

[...]

> >>>> I didn't say that.
> >>>> That would appear to be Oxyaena.
> >>>
> >>> It was. And you show no sign of disapproval.

...even after I quoted it to you. Are you afraid to tell us
what you think about it? I can sympathize with that, up to a
point. There is no telling what Oxyaena would do if you said
something negative about the use of the word "disease."

> >> I tend not to respond to empty trash talk, either by you or others.

Here comes that definition:

> > "trash talk" = personal criticism. Oxyaena called criticisms of
> > cladophilia a "disease". That is not personal, even though a lot
> > of the rest of Oxyaena's comment was.

You showed no disagreement with any of this. Shall I conclude
that you agree with my definition, and the fact that I am NOT
using trash talk just now?

> I tend not to respond to anything embedded in trash talk either. So I
> tend not to read stuff Oxyaena says to you.

I will hold off commenting on this until I see an answer to the
question I asked just now.

> >>> As I was hinting above, it takes two to tango.
> >>
> >> No idea what that means. Perhaps you should do more than hint.
> >
> > I mean, you are being uncommunicative about your attitude towards
> > what Oxyaena wrote. For all I know, this could just be a matter
> > of personal preferences, like Oxyaena suggesting Eight O'Clock coffee
> > when you prefer Starbucks.
>
> My attitude is that I don't like to read what Oxyaena says to you and
> often do not.

That is completely nonresponsive, the very antithesis of proactive.



<snip for focus>

> >> I enter when I have something interesting to say
> >> or am interested in getting an answer.
> >
> > That might explain why you aren't elaborating on
> > "no, no, no, and no" even now.

> The point of the OP was to get you to provide reasons for yes, yes, yes,
> and yes, because I'm not clear on what they would be.

I have explained them numerous times. On the other hand, all your
arguments for no, no, no and no that I can recall are mere echoes
of snarky comments by C. Patterson:

Cladists in general discourage the recognition of paraphyletic
groups. Patterson (1981, 1982) refers to them as unnatural
and no more than an artifact of taxonomists.
-Robert L. Carroll, _Vertebrate Paleontology and Evolution_, p. 11.

Carroll's next two pages run very counter to this pejorative dismissal
by Patterson. He even refers to a convention of Hennig
and others which he criticizes at length without stooping to such
pejorative talk. It was the convention that an ancestral species
becomes extinct as soon as a speciation event occurs to it.

Tell you what: I will let Carroll be my proxy for a start on what you
keep holding out for, an addition to my numerous arguments in favor of
paraphyletic groups.

That is, if you have access to the 1988 edition or at least pp. 12-13
thereof. Argue against what he writes there.


Concluded in next reply to this post of yours.

[John Harshman]

Your definition is not the usual one, but I'm happy to drop the personal
criticism. Can we talk about the supposed subject?

I refuse to psychoanalyze a third party. It's not relevant.

> Here, I deleted some text on which I expounded at length
> this morning.

?

>>>>>> I didn't say that.
>>>>>> That would appear to be Oxyaena.
>>>>>
>>>>> It was. And you show no sign of disapproval.
>
> ...even after I quoted it to you. Are you afraid to tell us
> what you think about it? I can sympathize with that, up to a
> point. There is no telling what Oxyaena would do if you said
> something negative about the use of the word "disease."

Here's what I think about it: I don't care what Oxyaena says.

>>>> I tend not to respond to empty trash talk, either by you or others.
>
> Here comes that definition:
>
>>> "trash talk" = personal criticism. Oxyaena called criticisms of
>>> cladophilia a "disease". That is not personal, even though a lot
>>> of the rest of Oxyaena's comment was.
>
> You showed no disagreement with any of this. Shall I conclude
> that you agree with my definition, and the fact that I am NOT
> using trash talk just now?

No. Please stop. The important thing is that it's off-topic, not that
it's trash topic. Back to the subject, please.

>> I tend not to respond to anything embedded in trash talk either. So I
>> tend not to read stuff Oxyaena says to you.
>
> I will hold off commenting on this until I see an answer to the
> question I asked just now.

This is sci.bio.paleontology, not alt.talk.psychoanalysis. Please, I beg
you, stop.

>>>>> As I was hinting above, it takes two to tango.
>>>>
>>>> No idea what that means. Perhaps you should do more than hint.
>>>
>>> I mean, you are being uncommunicative about your attitude towards
>>> what Oxyaena wrote. For all I know, this could just be a matter
>>> of personal preferences, like Oxyaena suggesting Eight O'Clock coffee
>>> when you prefer Starbucks.
>>
>> My attitude is that I don't like to read what Oxyaena says to you and
>> often do not.
>
> That is completely nonresponsive, the very antithesis of proactive.

Please.

>>>> I enter when I have something interesting to say
>>>> or am interested in getting an answer.
>>>
>>> That might explain why you aren't elaborating on
>>> "no, no, no, and no" even now.
>
>> The point of the OP was to get you to provide reasons for yes, yes, yes,
>> and yes, because I'm not clear on what they would be.
>
> I have explained them numerous times. On the other hand, all your
> arguments for no, no, no and no that I can recall are mere echoes
> of snarky comments by C. Patterson:
>
> Cladists in general discourage the recognition of paraphyletic
> groups. Patterson (1981, 1982) refers to them as unnatural
> and no more than an artifact of taxonomists.
> -Robert L. Carroll, _Vertebrate Paleontology and Evolution_, p. 11.
>
> Carroll's next two pages run very counter to this pejorative dismissal
> by Patterson. He even refers to a convention of Hennig
> and others which he criticizes at length without stooping to such
> pejorative talk. It was the convention that an ancestral species
> becomes extinct as soon as a speciation event occurs to it.
>
> Tell you what: I will let Carroll be my proxy for a start on what you
> keep holding out for, an addition to my numerous arguments in favor of
> paraphyletic groups.
>
> That is, if you have access to the 1988 edition or at least pp. 12-13
> thereof. Argue against what he writes there.

If you're unwilling to make an argument, I'll accept Carroll as a proxy.
At least Carroll is presumably on-topic. We'll see.

[Oxyaena]

On 8/14/2018 12:13 AM, John Harshman wrote:
Both of you keep making the baseless accusation that what I wrote was
full of personal attacks and baseless insults motivated by emotion
rather than logic. Here's a snippet of what I actually wrote for
documentation to show that this is *not* the case AT ALL:

> You may think it is flawed to think about relationships in any
> different way, but if so, I don't think you should discuss your
> family tree in everyday conversation. Especially not if there
> is a "long branch" leading to great-great grandchildren of a sibling of
> of yours, making them all more closely related to you than you
> are to your own grandparents.
>
>
>> something Linnaean taxonomy, with its emphasis on paraphyletic
>> solutions, wouldn't be able to do.
>
> It can however do a better job with relationships the way ordinary people
> discuss their relatives.

That's the whole reason why Linnaean taxonomy fails, because it doesn't
do a good job at explaining species-level or higher relationships
between taxa, only individuals. I am not on opposite sides here, Peter,
I too believe that modern taxonomy should be reformed or refined, with
less emphasis on ultra-cladistics, but I don't believe that Linnaean
taxonomy is the right way to do so."

Peter's probably going to keep on lying about it though, isn't he? After
all, he never responded to my response to him showing that I caught him
in a barefaced lie, and given that he's a pathological liar, he will
continue to ignore it.

[Peter Nyikos]

This is the third and final reply to this post of yours, John.

I was pleasantly surprised to see you get proactive in part of
your reply to this post of mine. That was the part to which I replied
yesterday morning.

However, it does suggest why you are so seldom proactive: you are
not very good at it.

In your reply yesterday, you found yourself abandoning proactive
comments you had made about "evolutionary trees" and "evolutionary
taxonomy with the words, "Tomato, tomahto." You left a similar
proactive comment about "phylogeny" high and dry, changing the
subject completely to cladophilia in response to what I had said
about it.

And I'm unable to make any sense out of your answer of "Yes and no"
to a question of mine. The rest of that sentence merely told
me whom to thank for that "Yes and no" answer.

That said, though, I give you an A for effort. The only way to
get good at any skill is to wade in and learn from your early
mistakes. And getting good at being proactive requires exactly
the sort of mental activity that has been recommended to retard
the onset of Alzheimer's. You had a very bad senior moment last
month about my knowledge of there being women paleontologists,
and this post sports another strange lapse of memory at the top.


Here, I snipped text that I handled in my first two replies: one
yesterday morning and another late yesterday evening. My mention
of the first post in the second one prompted a ? from you, suggesting
yet another memory lapse.

> Can we get back to paleontology?

That had already been started below, before you asked this question,
unless you mean "we" in a very restrictive sense.


About my replies to Ruben, I had written:

> > After seeing our exchange again, you might see its relevance to this thread.
> > However, it was the follow-up two posts later that is most relevant to this
> > "Paraphyly vs. Monophyly" thread:
> >
> > ________________________ repost _________________
> >
> > On Wednesday, August 1, 2018 at 1:16:36 PM UTC-4, ruben safir wrote:
> >> On 07/31/2018 08:47 AM, Peter Nyikos wrote:
> >>> "a non-avian, non-mammalian amniote."
> >>
> >> ROFL!
> >>
> >> It is interesting that an entire family that we all felt secure we
> >> understood, Reptiles, ended up a non-existing phylogetic group.
> >
> > You are well over a century behind the times, Ruben. A century ago,
> > no paleontologist worth his salt was ignorant of the fact that
> > mammals and birds descended from what was universally understood
> > to be the class Reptilia.
> >
> > But I don't think ANY paleontologist lost any sleep over the fact
> > that he was dealing in what is NOW called a "paraphyletic taxon."
> > I've often posted to s.b.p. about how Romer, near the beginning
> > of his classic _Vertebrate Paleontolgy_ (1945 edition) talked
> > about "horizontal" and "vertical" subdivisions of a phylogenetic
> > tree, and gave pros [1] and cons of each method.

See my proactive elaboration on this below.

> > The "horizontal" explicitly produced paraphyletic taxa, [2] the
> > "vertical" just as explicitly produced clades -- the only things
> > that Harshman and Oxyaena (and, if she is telling the truth, her husband)
> > will ever call "taxa".
> >
> > Over a century of systematics (when nobody thought there was
> > anything the matter with horizontal subdivisions that produced
> > paraphyletic taxa) shoved down the memory hole.
> >
> > [1] I'll gladly expound on the pros of the traditional classification,
> > if you are willing to listen.
>
> Go for it.

I was talking to Ruben, not you. Hence my comment about your use of
"we" up there.

> > [2] It has to be done the way Romer illustrated it, to avoid
> > polyphyletic taxa. Those were pretty well purged from the formal
> > classification, with the exception of Holostei, whose polyphyletic
> > nature was explicitly acknowledged by Romer [yes, he used the
> > word "polyphyletic"].
>
> I don't have the 1945 edition, just 1966. Are these illustrations the same?
>

You are back to being 0% proactive here. I have never seen the 1966 edition,
so I can't answer your question.

But do watch how I get proactive about the situation:

On p. 6 of the 1946 edition, there is a Fig. 1 which shows the same
small evolutionary tree cut up two different ways, the "vertical"
(cladistic, except for having actual genera/species at the nodes)
and the "horizontal" (showing a paraphyletic ancestral taxon, Family C).
It tells the pros and cons of each, and uses the words "closely related"
in a way antithetical to the cladophile-serving way: the way people
use the term in everyday life.

Can you find it in your 1966 edition?

> >> There
> >> are no reptiles. We have Archosaurs, Squamata, Synapsida, Mammals,
> >> Aves, Dinasoria, Testudinata..
> >
> > Your use of lower case "reptiles" makes this a fallacious pastiche of formal
> > and everyday usage.
> >
> >
> >> Turles, Snakes and Crocs are less related to each other than Birds and
> >> Crocs..
> >>
> >> What an amazing discovery.
> >
> > Done, and taken in its stride, before any of us was born.

With, of course, the cladophile-serving use of the words "less related".

> >
> > You have a lot of catching up to do. :-)
>
> It seems to me that you are underestimating how long it's been known
> that "Reptilia" is paraphyletic.

That's not what I was talking about. I was talking about both
birds and mammals, and I said "a century ago" in a different way,
because I didn't know how long ago it was first the "consensus"
that mammals are descended from reptiles [note the lower case].

> Certainly that was T. H. Huxley's view
> in the 1860s.

One man doth not a consensus make. But Huxley had primed the scientific
world for birds by calling them "glorified reptiles," and this
may have been the general "consensus" of his fellow anatomists by then,
so I won't quibble.
Reference:
https://en.wikisource.org/wiki/Picturesque_Dunedin/University_Museum

> What other sort of response were you looking for? I don't really see
> anything to talk about. Ruben was confused, you set him straight,

Interesting. You did not hesitate to criticize Ruben here, yet
you went through spectacular contortions to avoid criticizing
Oxyaena for the pejorative "disease" of "cladophobia".

> and in the process you alluded to an argument you might make for
> paraphyletic taxa. Nothing much to talk about until you
> actually make that argument.

I read this to say: nothing much I, John, want to talk about until you,
Peter, elaborate on some old arguments that Erik and I have seen you make
many times. That is, unless you, Peter, say you don't want to
elaborate on them, in which case I, John, will reluctantly
use Carroll's pp11-12 as a proxy elaboration on some of them.

Did I get that right?


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

[Oxyaena]

I love how you keep ignoring me responding to you with documentation
showing that you're a lying son of a bitch, so let me repost it here for
the third time in a row:

"> You may think it is flawed to think about relationships in any
> different way, but if so, I don't think you should discuss your
> family tree in everyday conversation. Especially not if there
> is a "long branch" leading to great-great grandchildren of a sibling of
> of yours, making them all more closely related to you than you
> are to your own grandparents.
>
>
>> something Linnaean taxonomy, with its emphasis on paraphyletic
>> solutions, wouldn't be able to do.
>
> It can however do a better job with relationships the way ordinary people
> discuss their relatives.

That's the whole reason why Linnaean taxonomy fails, because it doesn't
do a good job at explaining species-level or higher relationships
between taxa, only individuals. I am not on opposite sides here, Peter,
I too believe that modern taxonomy should be reformed or refined, with
less emphasis on ultra-cladistics, but I don't believe that Linnaean
taxonomy is the right way to do so."


>
>

[Peter Nyikos]

On Monday, August 13, 2018 at 1:40:47 PM UTC-4, Oxyaena wrote:
> ,
> >
> > "we" is inappropriate since you have consistently fought
> > against the word "cladophile", though not as emotionally
> > as Oxyaena.
>
> You deliberately lie about what I wrote to you as being merely
> "emotional".

"what I wrote to you" goes back about five years, to where you
first decided to target me for abuse under your old moniker
"Thrinaxodon." For the first year or so I was just scratching
my head, figuratively speaking, to figure out why you were doing
this, because you almost never tried to establish a firm connection
between anything I had done and the abuse that you showered on me.

What you reposted below is cherry-picked out of all the things
you've posted in reply to me, back when you were in a
"Dr. Oxyaena Jekyll" frame of mind.

There was no falsehood, let alone lying, involved in my
saying that this comment, made in your "Thrinaxodon Hyde"
frame of mind, was emotional:

I didn't read all the way through, since the cladophobe bullshit
infested every corner of my screen I quickly clicked out of it lest I
get your disease.
https://groups.google.com/d/msg/sci.bio.paleontology/RNINuDOndSM/cy3gGiLiBQAJ

This, I think, expresses your true attitude towards Linnean taxonomy,
complementing your polite but unscientific comments in response
to what I wrote and you are quoting below.

> What I actually wrote to you was this:

You lead off with quoting something I wrote, your own words
being further down:

> "> You may think it is flawed to think about relationships in any
> > different way, but if so, I don't think you should discuss your
> > family tree in everyday conversation. Especially not if there
> > is a "long branch" leading to great-great grandchildren of a sibling of
> > of yours, making them all more closely related to you than you
> > are to your own grandparents.
> >
> >> something Linnaean taxonomy, with its emphasis on paraphyletic
> >> solutions, wouldn't be able to do.
> >
> > It can however do a better job with relationships the way ordinary people
> > discuss their relatives.

Here was your response, using a cladophile-serving definition
of "relationships" and peremptorily rejecting Linnean *systematics*
[of which the ordinary everyday use of "closely related" is part;
see my reply to John today about Fig. 1 of Romer's 1945 text]:

> That's the whole reason why Linnaean taxonomy fails, because it doesn't
> do a good job at explaining species-level or higher relationships
> between taxa, only individuals.

It doesn't talk about individuals; it talks about species and higher
taxa in the same way that ordinary people talk about individuals.

> I am not on opposite sides here, Peter,
> I too believe that modern taxonomy should be reformed or refined, with
> less emphasis on ultra-cladistics,

What do you include under this term? Emotional outbursts
like the one to which I was actually referring?

John seems to think of cladophilia as a "big tent," tolerating
without murmur such emotional, ideological outbursts in order
to reserve all the energy of its movers and shakers to marginalizing
anyone who objects to the intolerance of paraphyletic taxa. Also, to
the commandeering of terms like "more closely related" in a
"scientific" version of the use of Newspeak in George Orwell's _1984_.

> but I don't believe that Linnaean
> taxonomy is the right way to do so."
>
> Here's one of the many pieces of documentation that you request which
> can be easily found by scrolling through a fucking thread.

So can my repeatedly referring to your outburst in my replies
to John this past week or so.

You're
> probably going to ignore this, since it is contrary to the picture you
> portray of me, as a raging berserker, but since when did honesty
> actually matter to you, Nyikos?

It has always mattered to me. Were I like you, I would accuse you
of deliberately choosing an innocent, friendly but still ideologically
motivated comment, with the full knowledge that I was actually referring to
your outburst, just so you could vent your spleen against me.


As it is, I merely ask: why did you cherry-pick the exchange you did,
without caring about what else had transpired between us?


Peter Nyikos
Professor of Mathematics -- standard disclaimer--
Univ. of So. Carolina
http://people.math.sc.edu

[Oxyaena]

On 8/14/2018 12:48 PM, Peter Nyikos wrote:
> On Monday, August 13, 2018 at 1:40:47 PM UTC-4, Oxyaena wrote:
>> ,
>>>
>>> "we" is inappropriate since you have consistently fought
>>> against the word "cladophile", though not as emotionally
>>> as Oxyaena.
>>
>> You deliberately lie about what I wrote to you as being merely
>> "emotional".
>
> "what I wrote to you" goes back about five years, to where you
> first decided to target me for abuse under your old moniker
> "Thrinaxodon." For the first year or so I was just scratching
> my head, figuratively speaking, to figure out why you were doing
> this, because you almost never tried to establish a firm connection
> between anything I had done and the abuse that you showered on me.
>
> What you reposted below is cherry-picked out of all the things
> you've posted in reply to me, back when you were in a
> "Dr. Oxyaena Jekyll" frame of mind.

You must love portraying the people you hate the most as two-dimensional
monsters and not as actually being multifaceted people.

>
> There was no falsehood, let alone lying, involved in my
> saying that this comment, made in your "Thrinaxodon Hyde"
> frame of mind, was emotional:
>
> I didn't read all the way through, since the cladophobe bullshit
> infested every corner of my screen I quickly clicked out of it lest I
> get your disease.
> https://groups.google.com/d/msg/sci.bio.paleontology/RNINuDOndSM/cy3gGiLiBQAJ
>
> This, I think, expresses your true attitude towards Linnean taxonomy,
> complementing your polite but unscientific comments in response
> to what I wrote and you are quoting below.

Specify, how exactly is what I wrote "unscientific".

>
>
>> What I actually wrote to you was this:
>
> You lead off with quoting something I wrote, your own words
> being further down:
>
>> "> You may think it is flawed to think about relationships in any
>> > different way, but if so, I don't think you should discuss your
>> > family tree in everyday conversation. Especially not if there
>> > is a "long branch" leading to great-great grandchildren of a sibling of
>> > of yours, making them all more closely related to you than you
>> > are to your own grandparents.
>> >
>> >> something Linnaean taxonomy, with its emphasis on paraphyletic
>> >> solutions, wouldn't be able to do.
>> >
>> > It can however do a better job with relationships the way ordinary people
>> > discuss their relatives.
>
> Here was your response, using a cladophile-serving definition
> of "relationships" and peremptorily rejecting Linnean *systematics*
> [of which the ordinary everyday use of "closely related" is part;
> see my reply to John today about Fig. 1 of Romer's 1945 text]:
>

You ignore what I explained to you in that thread, that arbitrarily
putting all pre-Cenozoic monotremes in a single clade, even if certain
monotremes are more closely related to platypuses than to echidnas,
doesn't accurately show evolutionary relationships, instead giving the
false impression that all pre-Cenozoic monotremes were part of one
clade, and their descendants another clade.

>> That's the whole reason why Linnaean taxonomy fails, because it doesn't
>> do a good job at explaining species-level or higher relationships
>> between taxa, only individuals.
>
> It doesn't talk about individuals; it talks about species and higher
> taxa in the same way that ordinary people talk about individuals.
>
>
>> I am not on opposite sides here, Peter,
>> I too believe that modern taxonomy should be reformed or refined, with
>> less emphasis on ultra-cladistics,
>
> What do you include under this term? Emotional outbursts
> like the one to which I was actually referring?

It was sarcasm, jackass. Are you *that* fucking literal?

>
> John seems to think of cladophilia as a "big tent," tolerating
> without murmur such emotional, ideological outbursts in order
> to reserve all the energy of its movers and shakers to marginalizing
> anyone who objects to the intolerance of paraphyletic taxa. Also, to
> the commandeering of terms like "more closely related" in a
> "scientific" version of the use of Newspeak in George Orwell's _1984_.
>

Here you clearly show your coinage and usage of the term "cladophilia"
is emotionally rather than scientifically motivated.

>
>> but I don't believe that Linnaean
>> taxonomy is the right way to do so."
>>
>> Here's one of the many pieces of documentation that you request which
>> can be easily found by scrolling through a fucking thread.
>
> So can my repeatedly referring to your outburst in my replies
> to John this past week or so.
>
> You're
>> probably going to ignore this, since it is contrary to the picture you
>> portray of me, as a raging berserker, but since when did honesty
>> actually matter to you, Nyikos?
>

> It has always mattered to me. [snip baseless accusations]


Bullshit noted.

>
> As it is, I merely ask: why did you cherry-pick the exchange you did,
> without caring about what else had transpired between us?

I picked it from a particular post because I thought it did a good job
of showing that you weren't giving the whole picture of what transpired
between us, it doesn't help that in the post I was replying to you had
snipped about half of what I wrote as you usually do.

[Peter Nyikos]

On Thursday, August 2, 2018 at 11:15:34 AM UTC-4, erik simpson wrote:

> On Wednesday, August 1, 2018 at 8:28:36 PM UTC-7, John Harshman wrote:
> > Rather than clog up a thread on pterosaurs, let's argue about the
> > benefits of paraphyly vs. monophyly here. There are several
> > distinguishable issues:
> >
> > 1. Can paraphyletic groups be more useful in classification than strict
> > adherence to monophyly?
> >

> > 2. Should particular fossil "species" be declared to be ancestors or
> > ancestor candidates, and if so, what is gained?
> >

> > 3. Is it useful to declare higher taxa ancestral to other taxa?
> >

> > 4. Are "evolutionary trees" (in which taxa are ancestral, either by
> > placing species at internal nodes or by having taxa emerge from
> > "bubbles") ever more useful than phylogenetic trees (i.e. cladograms
> > with or without meaningful branch lengths)?
> >
> > Discuss. My answers of course would be no, no, no, and no.
>

> There aren't very many of us even present here any more, and I think we all know

> what everyone else thinks about these (valid) considerations. The "war" in
> paleontology more generally was fought a long time ago, and the outcome is
> well-known.

Huh? Wasn't paleontology just swept away in the flood of
"the cladistic wars," carried on mostly by systematists
who were, at best, amateur paleontologists (and that in the minority
of cases)?

We are also all aware of the dissenter among us, whose postions
> seem not to have varied significantly since 1945 (an important publication date
> for Romer's tome).

In case you are curious as to why I am so slow in supporting Yes
answers (as opposed to criticism of the wording of two of the questions,
which no one seems to have adequately addressed) to Harshman's
four questions...

...it is because you have poisoned the wells with factually
false trash talk like this.


> This can't be, because our dissenter hadn't been born at
> that time, or was still an infant. He hasn't mentioned overlapping
> paraphyletic groups for a while, so perhaps his opinions have evolved over time, but the
> recent instances of his credo sound much the same as the many repetitions he's
> posted before.

Don't worry, I'll start supporting Yes answers before the week is out,
and then you can have all the fun you want at my expense, e.g.,

See? see? I TOLD everyone Peter will just be repeating
his old arguments. We're just wasting our time reading
what he has to say.


> If there is more to discuss about pterosaurs, let's do that instead. This
> thread will either die quickly if he ignores it, or become ugly and rancorous,
> go on for a long time and get nowhere.

It's already gotten somewhere. People have gotten to see a side of
John Harshman that I, at least, never suspected. It is in a post
where he completely ignored the following statement by myself:

_________________excerpt from John's reply, nothing deleted_________

> I have explained them numerous times. On the other hand, all your
> arguments for no, no, no and no that I can recall are mere echoes
> of snarky comments by C. Patterson:
>
> Cladists in general discourage the recognition of paraphyletic
> groups. Patterson (1981, 1982) refers to them as unnatural
> and no more than an artifact of taxonomists.
> -Robert L. Carroll, _Vertebrate Paleontology and Evolution_, p. 11.
>
> Carroll's next two pages run very counter to this pejorative dismissal
> by Patterson. He even refers to a convention of Hennig
> and others which he criticizes at length without stooping to such
> pejorative talk. It was the convention that an ancestral species
> becomes extinct as soon as a speciation event occurs to it.

===================================================================

John had nothing to say about Hennig's convention, and I suppose you
don't either.

But you just KNOW John has powerful arguments up his sleeve
-- beyond his (and your) paraphrases of Patterson -- for his answers
of no, no, no, and no, don't you?

Peter Nyikos
Professor of Mathematics -- standard disclaimer--

University of South Carolina
http://people.math.sc.edu

[Oxyaena]

On 8/15/2018 7:17 AM, Peter Nyikos wrote:

Why are you wasting everyone's time ranting about your pet peeves
against cladistics, when you could actually be doing something
constructive like responding to the posts about paleontology I just put up?

[Peter Nyikos]

Your whole argument rests on endless repetition of a claim that
rests on a self-serving, unhistorical, arbitrary and unscientific
use of the term "more closely related."

But

[Peter Nyikos]

Because the "indignant" replies to me that you keep making on this thread,
and on the "Pterosaur dietary hypotheses" thread, seem to mean
far more to you than either paleontology or cladistics.

Peter Nyikos

[Oxyaena]

[crickets]

Is anybody surprised?

[Oxyaena]

So you admit you don't give a shit about actually disucssing on-topic
material and would rather flame me? Not surprised.

[John Harshman]

On 8/15/18 4:17 AM, Peter Nyikos wrote:

> Huh? Wasn't paleontology just swept away in the flood of
> "the cladistic wars," carried on mostly by systematists
> who were, at best, amateur paleontologists (and that in the minority
> of cases)?

No. The cladist wars hit different fields at different times, and the
battles were all internal to those fields. Your acquaintance with the
events is apparently minimal and is probably colored by your desire that
the outcome be illegitimate.

> Don't worry, I'll start supporting Yes answers before the week is out,

Excellent.

> John had nothing to say about Hennig's convention, and I suppose you
> don't either.

Hennig's convention is irrelevant to cladistic classification,
paraphyletic groups, etc. It's irrelevant because of two things: 1)
species are not generally defined by monophyly but by propensity to
interbreed, which is plesiomorphic, and, more importantly, 2) we can't
identify ancestors in the fossil record, and the convention relies on
placing actual taxa at internal nodes.

[Peter Nyikos]

On Wednesday, August 15, 2018 at 8:37:18 AM UTC-4, Oxyaena wrote:
> On 8/15/2018 7:27 AM, Peter Nyikos wrote:

This is priceless. This second attribution line
is to the following post, from which you quoted nothing:

_______________________begin included post_________________

On Wednesday, August 15, 2018 at 7:19:24 AM UTC-4, Oxyaena wrote:
> On 8/15/2018 7:17 AM, Peter Nyikos wrote:
>
> Why are you wasting everyone's time ranting about your pet peeves
> against cladistics, when you could actually be doing something
> constructive like responding to the posts about paleontology I just put up?

Because the "indignant" replies to me that you keep making on this thread,
and on the "Pterosaur dietary hypotheses" thread, seem to mean
far more to you than either paleontology or cladistics.

Peter Nyikos

========================== end of post archived at:
https://groups.google.com/d/msg/sci.bio.paleontology/nNhyCBvm_9k/qWbYA8RfDAAJ
Date: Wed, 15 Aug 2018 04:40:18 -0700 (PDT)
Message-ID: <59f690d9-fee0-46f2...@googlegroups.com>
Subject: Re: Paraphyly vs. Monophyly

As if to prove me right, you couldn't resist yet another
"indignant" reply, in the "crickets" repost style of your
number one spin doctor, Bob Casanova. In other words,
you were showing how remiss I've supposedly been in not
replying to it yet.

Why didn't you also tout the benefits of your latest post again?

Is it because that post really wasn't about paleontology, it was
about evolution? Did you suddenly remember that, after Ruben Safir
posted on another aspect of evolution, you made no comment on
its contents, but only asked him what this had to do with paleontology?


If so, there may be hope for your weaning yourself from double
standards and hypocrisy.


Like I told your number one spin doctor last night, I don't
reply to twits like him (and you) on your timetables. The rest of
your repost goes unanswered, and the original will be replied to on
my own good time -- not yours.


Peter Nyikos

[Peter Nyikos]

My apologies. I meant to hit "Discard" and hit "Post" instead.
I had decided there were more important things to respond to,
like Harshman's post of two days ago that I haven't answered yet. Even
that will have to wait until later today.

Like I told Oxyaena a few minutes ago, I will respond to the
rest of her/his post [snipped, below] on my own good time.

Peter Nyikos

[Peter Nyikos]

On Wednesday, August 15, 2018 at 10:12:23 AM UTC-4, Peter Nyikos wrote:
> On Wednesday, August 15, 2018 at 8:37:18 AM UTC-4, Oxyaena wrote:
> > On 8/15/2018 7:27 AM, Peter Nyikos wrote:
>
> This is priceless. This second attribution line
> is to the following post, from which you quoted nothing:

My mistake: I didn't realize that another post had been accidentally
made by me, and that the following post simply hadn't been replied
to at all.

But most of what you see below was quite appropriate, including the
failure of Oxyaena to again tout a post that was claimed to be about
paleontology, but really wasn't.

[Oxyaena]

On 8/15/2018 10:12 AM, Peter Nyikos wrote:
[snip personal attacks and baseless insults by dipshit]
>
>
> Peter Nyikos

Do you get off on trying to provoke other people? Is the fact that you
don't reply to our "timetables" somehow because you know we're right?
You never did actually address the part where I caught you in a lie
about the context of our discussion on the pterosaur thread, and I
provided sufficient documentation. It's cute how you run away like the
little coward you are when confronted with your bullshit.

Also, cladistics isn't paleontology either, so maybe you should refrain
from calling me a hypocrite.

[Oxyaena]

On 8/15/2018 10:25 AM, Peter Nyikos wrote:
> On Wednesday, August 15, 2018 at 10:12:23 AM UTC-4, Peter Nyikos wrote:
>> On Wednesday, August 15, 2018 at 8:37:18 AM UTC-4, Oxyaena wrote:
>>> On 8/15/2018 7:27 AM, Peter Nyikos wrote:
>>
>> This is priceless. This second attribution line
>> is to the following post, from which you quoted nothing:
>
> My mistake: I didn't realize that another post had been accidentally
> made by me, and that the following post simply hadn't been replied
> to at all.
>
> But most of what you see below was quite appropriate, including the
> failure of Oxyaena to again tout a post that was claimed to be about
> paleontology, but really wasn't.

Cladistics isn't paleontology either, you hypocritical asshole.

[Oxyaena]

Which means "never".


> Peter Nyikos
>

[Peter Nyikos]

On Wednesday, August 15, 2018 at 11:56:55 AM UTC-4, Oxyaena wrote:
> On 8/15/2018 10:25 AM, Peter Nyikos wrote:
> > On Wednesday, August 15, 2018 at 10:12:23 AM UTC-4, Peter Nyikos wrote:
> >> On Wednesday, August 15, 2018 at 8:37:18 AM UTC-4, Oxyaena wrote:
> >>> On 8/15/2018 7:27 AM, Peter Nyikos wrote:
> >>
> >> This is priceless. This second attribution line
> >> is to the following post, from which you quoted nothing:
> >
> > My mistake: I didn't realize that another post had been accidentally
> > made by me, and that the following post simply hadn't been replied
> > to at all.
> >
> > But most of what you see below was quite appropriate, including the
> > failure of Oxyaena to again tout a post that was claimed to be about
> > paleontology, but really wasn't.
>
>
> Cladistics isn't paleontology either, you hypocritical asshole.

Your comment is such a weird non sequitur, it looks like you
need to get back on meds.

Peter Nyikos

[Peter Nyikos]

On Wednesday, August 15, 2018 at 8:38:16 AM UTC-4, Oxyaena wrote:
> On 8/15/2018 7:40 AM, Peter Nyikos wrote:
> > On Wednesday, August 15, 2018 at 7:19:24 AM UTC-4, Oxyaena wrote:
> >> On 8/15/2018 7:17 AM, Peter Nyikos wrote:
> >>
> >> Why are you wasting everyone's time ranting about your pet peeves
> >> against cladistics, when you could actually be doing something
> >> constructive like responding to the posts about paleontology I just put up?

"posts" is plural, yet the one you "just (now)" had put up when you
said this was not about paleontology at all, while the one before that
was a specialized one on Felidae that I don't have anything to add to.

> >
> > Because the "indignant" replies to me that you keep making on this thread,
> > and on the "Pterosaur dietary hypotheses" thread, seem to mean
> > far more to you than either paleontology or cladistics.
> >
> > Peter Nyikos
> >

You do not deny that they mean far more to you, but jump to a weird
conclusion instead.

> So you admit you don't give a shit about actually disucssing on-topic
> material and would rather flame me? Not surprised.

You were proudly touting YOUR posts, and that's ALL I was referring to.

And this whole thread is primarily on cladistic vs traditional classification
methods, and I have been discussing them with Harshman. You are strangely absent from that discussion.

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --
U. of South Carolina at Columbia
http://www.math.sc.edu/~nyikos/

[Peter Nyikos]

On Wednesday, August 15, 2018 at 9:49:37 AM UTC-4, John Harshman wrote:
> On 8/15/18 4:17 AM, Peter Nyikos wrote:
>
> > Huh? Wasn't paleontology just swept away in the flood of
> > "the cladistic wars," carried on mostly by systematists
> > who were, at best, amateur paleontologists (and that in the minority
> > of cases)?
>
> No. The cladist wars hit different fields at different times, and the
> battles were all internal to those fields.

Thank you for this information.

> Your acquaintance with the
> events is apparently minimal and is probably colored by your desire that
> the outcome be illegitimate.

Only the ideological part.

As for the scientific part, I keep reading bits and pieces about
the "cow - lungfish - salmon" debate, but from what I've read,
the traditional systematists picked a lousy third taxon. They
could have done a lot better to pick the bichir *Polypterus*
for that third taxon.

Worse yet, they either did not know how Romer 1945 used the term
"closely related " in a completely different way than the
way I've seen it used in every account I've seen so far,
or else we have another example of "history is written by the victors."

That reminds me: did you see whether the 1966 edition has something
fitting the description I gave you of Fig. 1 of the 1945 edition
in a post of yesterday? You haven't replied to that post yet.

> > Don't worry, I'll start supporting Yes answers before the week is out,
>
> Excellent.
>
> > John had nothing to say about Hennig's convention, and I suppose you
> > don't either.
>
> Hennig's convention is irrelevant to cladistic classification,
> paraphyletic groups, etc.

What do you mean? As Carroll points out on p. 13, the result of
this convention is that almost exactly half of all species that
ever existed were paraphyletic.

Another offshoot of this convention is to use the term "hypothetical"
for all of them, as though that made them somehow outside the field
of science, and safely "out of sight [except for all those pesky
nodes], out of mind".

> It's irrelevant because of two things: 1)
> species are not generally defined by monophyly but by propensity to
> interbreed, which is plesiomorphic,

I fail to see the relevance, unless you are referring to the convention
that no named species should ever have been subject to speciation.
And that segues into my reply to your next point.

> and, more importantly, 2) we can't
> identify ancestors in the fossil record, and the convention relies on
> placing actual taxa at internal nodes.

The irony is that, say, a clade of 8 species would have 7 or 8 paraphyletic
species hidden away in the nodes by the convention, while there
might in reality be only one paraphyletic species involved, and
be mistaken for one of the "actual taxa" because it is still alive.

And you call yourselves "objective" and "scientific" while denying
those terms to traditional systematists!


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

PS I was going to start replying to the one other post of yours
on this thread to which I haven't replied yet, but the rest of
this evening is taken up with my family. Tomorrow, then.

[Peter Nyikos]

Oxyaena's bizarre *non sequitur* of yesterday had its precedents
already back here. This suggests that 'e's been in need of meds
for over a week now.

On Wednesday, August 8, 2018 at 2:27:10 AM UTC-4, Oxyaena wrote:

> On 8/7/2018 11:13 PM, John Harshman wrote:
> > On 8/7/18 5:42 PM, Peter Nyikos wrote:

> >> On Wednesday, August 1, 2018 at 11:28:36 PM UTC-4, John Harshman wrote:
> >>> Rather than clog up a thread on pterosaurs, let's argue about the
> >>> benefits of paraphyly vs. monophyly here. There are several
> >>> distinguishable issues:
> >>>
> >>> 1. Can paraphyletic groups be more useful in classification than strict
> >>> adherence to monophyly?
> >>

> >> Poorly worded. Ever since 2002 all I have ever argued for was for
> >> cladophiles like you not to ban paraphyletic groups, but to admit
> >> them side by side with monophyletic ones, because they also
> >> contribute to our understanding of evolution.
> >

> > It isn't quite clear what "side by side" means. Are you proposing two
> > parallel classification systems, one with strict monophyly and one
> > allowing paraphyly? To me, that just seems redundant. If that's what you
> > mean.

> >
> >>> 2. Should particular fossil "species" be declared to be ancestors or
> >>> ancestor candidates, and if so, what is gained?
> >>>
> >>> 3. Is it useful to declare higher taxa ancestral to other taxa?
> >>

> >> Also poorly worded. It is not the higher taxa, but species not
> >> yet discovered that are WITHIN those taxa that are ancestral
> >> even to such spectacular taxa as tetrapoda. We already have two
> >> genera, Tiktaalik and another whose name begins with E that are
> >> very likely in the same family, maybe even subfamily (as the old-timers
> >> reckoned these things, as an actual ancestor of all members of
> >> the crown group Tetrapoda, and many terrestrial vertebrates outside it.
> >
> > How would you determine if these species are in the same family or
> > subfamily as the ancestor? And what is gained?

> >
> >>> 4. Are "evolutionary trees" (in which taxa are ancestral, either by
> >>> placing species at internal nodes or by having taxa emerge from
> >>> "bubbles") ever more useful than phylogenetic trees (i.e. cladograms
> >>> with or without meaningful branch lengths)?
> >>>
> >>> Discuss. My answers of course would be no, no, no, and no.
> >>

> >> Sans discussion, I see.
> >
> > That's because I would like to hear your arguments. Please give your
> > arguments.
> >
> >> As you know, I have given rational arguments for all of the above, and
> >> now I'd like to see rational arguments for these negative answers.
> >
> > Sorry, but I do not recall you giving any rational arguments. We
> > probably disagree on what's rational. I was inviting you to give it your
> > best shot.

> >
> >> And I don't mean emotional arguments like the following, which
> >> only lends support to the thesis that your negative answers
> >> are ideologically and not scientifically based.
> >>

> >> I didn't read all the way through, since the cladophobe bullshit
> >> infested every corner of my screen I quickly clicked out of it
> >> lest I
> >> get your disease.
> >> https://groups.google.com/d/msg/sci.bio.paleontology/RNINuDOndSM/cy3gGiLiBQAJ
> >>
> >

> > How does this lend support to any thesis about me? I didn't say that.

> > That would appear to be Oxyaena.
>

> I wrote it, it has nothing to do with this thread, ergo usual Nyikosian
> drivel,

This is already peculiar, talking myopically about this thread
when the issue of this thread is parapyly vs. monophyly,
and the comment is about paraphyly ("cladophobe").

What's more, the "ergo" indicates a literal *non sequitur*.


> and it was in response to his irrational response to my initial
> post, which was extremely polite (he likes to leave that out)

This seriously suggests that you have lost contact with reality.
Here is what you had written in the post to which I had been
replying:

Yes, I do, and it isn't denial, fuckwad. I never insulted you in
this post, but apparently you're all too willing to act like the
immature sociopath you are rather than leave sbp out of the
nonsense you conduct in talk.origins.
https://groups.google.com/d/msg/sci.bio.paleontology/RNINuDOndSM/Yqpa_BOWBQAJ

Wait, there's more from the same post:

Once again, you lie about having never seen it. I was the one who
came to you to propose to let bygones be bygones. Your apparent self-
serving memory is intact, Nyikos.
Message-ID: <pjq959$p7a$1...@gioia.aioe.org>

By the way, this was where I finally found out that the policy you
had been referring to was utterly unlike the one that Harshman, Norman,
Simpson, and myself agreed on over 4 years ago. And bizarrely interpreted
by yourself, to boot.


And still more, from the same post:
So you admit you'd rather insult me than partake in constructive
discussion on paleontology, since you haven't replied to any of my
otherr posts here yet.
Subject: Re: Pterosaur dietary hypotheses
Date: Tue, 31 Jul 2018 14:18:29 -0400

Of course, there was no such admission. This kind of "you admit" illogic
is part and parcel of the tactics of some of the blackguards with whom you
are allied in talk.origins, especially jillery.

And it is a common theme all through these last several weeks: you
hungering for recognition for your posts on paleontology [1]
while simultaneously gloating over how you must be right about
catching me in a lie since I haven't responded to an ABUSIVE
post on your private timetable.

[1] But there was one you said was on paleontology, but it
was on evolution instead, band when I pointed this out,
you came out with your non sequitur that was so weird,
I told you that you need to get back on your meds.

> on the
> Pterosaur thread. Ignore when he does this, it only feeds the troll.

I've been feeding the real troll -- yourself -- because you've
been insisting that I feed you, on pain of being labeled a lying
scumbag by yourself.


> >
> >> I had written:
> >> By the way, you haven't responded to my post of yesterday
> >> in reply to Ruben Safir, even though there was actual
> >> paleontology at the end, not just systematics. Can you say "double
> >> standard"?
> >> --- from the Pterosaur thread to which you refer at the beginning

Not only "double standard" but also "hypocrite" since you had
been on my case for not replying to your posts on paleontology,
and you keep demanding recognition for the "on-topic" posts you do.

> >> And the response was what you are reading above.

Peter Nyikos

[Peter Nyikos]

Same song, second verse:

On Wednesday, August 8, 2018 at 2:34:43 AM UTC-4, Oxyaena wrote:
> On 8/7/2018 11:13 PM, John Harshman wrote:
> > On 8/7/18 5:42 PM, Peter Nyikos wrote:

[snip some context, included in my reply to Oxyaena's preceding post]

> >> And I don't mean emotional arguments like the following, which
> >> only lends support to the thesis that your negative answers
> >> are ideologically and not scientifically based.
> >>
> >> I didn't read all the way through, since the cladophobe bullshit
> >> infested every corner of my screen I quickly clicked out of it
> >> lest I
> >> get your disease.
> >> https://groups.google.com/d/msg/sci.bio.paleontology/RNINuDOndSM/cy3gGiLiBQAJ
> >>
> >
> > How does this lend support to any thesis about me? I didn't say that.
> > That would appear to be Oxyaena.
> >

> >> I had written:
> >> By the way, you haven't responded to my post of yesterday
> >> in reply to Ruben Safir, even though there was actual
> >> paleontology at the end, not just systematics. Can you say "double
> >> standard"?
> >> --- from the Pterosaur thread to which you refer at the beginning
> >>

> >> And the response was what you are reading above.
> >

> > Not my response, though.
>
> I should also add that he left out *why* I disagree with him on this
> issue, namely that Linnaean taxonomy doesn't do a good job of
> representing evolutionary relationships, cladistics does a far better
> job at it, since Linnaean taxonomy would place chimps and other apes in
> Pongo,

Pongo is the scientific name for the orangutan.

You mean Pongidae. But even that would probably have been changed
by now, were Linnean classification not so universally despised.
After all, it came to reject "Pithecanthropus" and put it in
*Homo erectus*.

This is because we now have much better information on evolutionary
relationships, which were once so obscure that the female of Sivapithecus
was once given a different genus name, Ramapithecus, and was widely
believed to be in the ancestral line to Homo.

It is now known to be to be in a clade with

--wait for it --

Pongo!
and in a clade different from the {chimp, gorilla, human} clade.

> while cladistics does a better job at accurately showing
> evolutionary relationships between taxa, so chimps and humans will be
> placed in a clade, with gorillas as an offshoot of the clade and
> orangutans being the sister group to the clade.

I do believe that if Linnean classification were pursued by more than
a tiny handful of severely marginalized systematists, all this
would be reflected in it by now. In fact, all they would have to
do is to adopt the very names that are now in use -- Hominidae,
Homininae, Homini, Homo.

And maybe they have -- but I don't think there will ever be
a comprehensive Linnean classification again, thanks to the
intolerance of "almost everyone" as Harshman puts it.


Now comes another weird *non sequitur*:

> In short, he's being a dishonest prick

...by failing to give you credit for things having nothing to
do with your nasty remark, which primarily served as your
excuse for not talking about the paleontology in my reply
to Ruben.

And you have kept to that excuse to this day, the excuse
that you stopped reading before you got to it.


> and should be ignored, as I am
> refusing to respond to him since he gets on my nerves.

This resolution was broken, then followed by a killfile
announcement which was abandoned the following day,
and you never returned to your original refusal.

Quite the contrary: you keep insisting that I reply
to posts of yours, knowing full well that any reply
I make to you will be followed by another abusive
post by you, and so on ad infinitum.

It's almost as if you ENJOY how I get on your nerves!


> I wrote my
> flippant remark after several posts engaging him on this issue,

All a broken record routine of "it shows relationships [NOT used
the way Romer used the words "closely related"] better than
the Linnean." This was all the engagement you have ever given
me on this issue.


> my patience wore thin, I had explained to him in-depth why he was wrong
> *politely* several times,

Endless repetitions of "it shows relationships better" is not "in-depth".

And in an earlier post, you had already written the following
put-downs:


You wouldn't know, since you've never done any fieldwork.


[snip idiocy]

Cladophilia doesn't
exist. Just because you have a problem with the current scientific
consensus doesn't mean jack shit in the long run.

> and he kept up his bullshit like I had never
> even wrote what I did. You should discount him mentioning me, it has
> nothing to do with you and is only him being a libelous piece of shit.

Now I am guilty of libel for not having mentioned your broken record
routine. You really need to see a counselor, Oxyaena.

Maybe your spouse would serve as one, were you to show him
these last two posts of mine.


> It's also the same thread where I read him the riot act saying I will no
> longer play his games. You should do the same.

I don't play games. If you don't see yourself as playing a game,
you are really in need of in-depth [and I do mean IN-DEPTH]
counseling.

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

PS I was going to do an on-topic reply to Harshman first thing
this morning, then these two sickeningly self-serving posts
of yours caught my eye.

[John Harshman]

On 8/15/18 6:26 PM, Peter Nyikos wrote:
> On Wednesday, August 15, 2018 at 9:49:37 AM UTC-4, John Harshman wrote:
>> On 8/15/18 4:17 AM, Peter Nyikos wrote:
>>
>>> Huh? Wasn't paleontology just swept away in the flood of
>>> "the cladistic wars," carried on mostly by systematists
>>> who were, at best, amateur paleontologists (and that in the minority
>>> of cases)?
>>
>> No. The cladist wars hit different fields at different times, and the
>> battles were all internal to those fields.
>
> Thank you for this information.
>
>> Your acquaintance with the
>> events is apparently minimal and is probably colored by your desire that
>> the outcome be illegitimate.
>
> Only the ideological part.
>
> As for the scientific part, I keep reading bits and pieces about
> the "cow - lungfish - salmon" debate, but from what I've read,
> the traditional systematists picked a lousy third taxon. They
> could have done a lot better to pick the bichir *Polypterus*
> for that third taxon.

Why? And what have you been reading?

> Worse yet, they either did not know how Romer 1945 used the term
> "closely related " in a completely different way than the
> way I've seen it used in every account I've seen so far,
> or else we have another example of "history is written by the victors."
>
> That reminds me: did you see whether the 1966 edition has something
> fitting the description I gave you of Fig. 1 of the 1945 edition
> in a post of yesterday? You haven't replied to that post yet.

Yes, I saw it, and I suspect the text didn't change either. To the
extent Romer's text contains an argument for paraphyly, that argument is
seriously flawed. Ironically, the inclusion of fossils makes it more
flawed than if he had considered only extant species.

>>> Don't worry, I'll start supporting Yes answers before the week is out,
>>
>> Excellent.
>>
>>> John had nothing to say about Hennig's convention, and I suppose you
>>> don't either.
>>
>> Hennig's convention is irrelevant to cladistic classification,
>> paraphyletic groups, etc.
>
> What do you mean? As Carroll points out on p. 13, the result of
> this convention is that almost exactly half of all species that
> ever existed were paraphyletic.
>
> Another offshoot of this convention is to use the term "hypothetical"
> for all of them, as though that made them somehow outside the field
> of science, and safely "out of sight [except for all those pesky
> nodes], out of mind".

I am unable to interpret that statement. But no, the hypothetical nature
of internal nodes has nothing at all to do with Hennig's convention, so
perhaps I don't have to understand your attempted point. The reason
internal nodes are hypothetical is that we can't assign actual species
to them, and thus we avoid making claims that can't be supported by the
data. What we can make claims about would be the character states at
those nodes, which can be turned into a description of that unknown
ancestor. Of course that description is an estimate, as everything in
science.

>> It's irrelevant because of two things: 1)
>> species are not generally defined by monophyly but by propensity to
>> interbreed, which is plesiomorphic,
>
> I fail to see the relevance, unless you are referring to the convention
> that no named species should ever have been subject to speciation.
> And that segues into my reply to your next point.

There is no such convention, so again I can't interpret that statement.
The relevance is that species are a special sort of taxon. All other
taxa are defined as clades, but species are not.

There is also a problem with defining species when you extend them over
space and time. Regarding space, consider ring species. And the same
sort of gradual transition resulting in discontinuity, over time rather
than space, is much more common.

>> and, more importantly, 2) we can't
>> identify ancestors in the fossil record, and the convention relies on
>> placing actual taxa at internal nodes.
>
> The irony is that, say, a clade of 8 species would have 7 or 8 paraphyletic
> species hidden away in the nodes by the convention, while there
> might in reality be only one paraphyletic species involved, and
> be mistaken for one of the "actual taxa" because it is still alive.

I don't understand that either, but since nobody is defending that silly
convention there seems no point.

> And you call yourselves "objective" and "scientific" while denying
> those terms to traditional systematists!

Yes. I don't understand what argument you are making that cladistic
classification isn't objective or scientific, or perhaps that
traditional classification is either.

I exhort you to greater effort to make your arguments clear. Now much of
my current confusion may have to do with your proceeding from false
premises, but I don't think all of it is.

[Oxyaena]

On 8/16/2018 7:54 AM, Peter Nyikos wrote:
[snip personal attacks and baseless accusations by Nyikos]

>
> PS I was going to do an on-topic reply to Harshman first thing
> this morning, then these two sickeningly self-serving posts
> of yours caught my eye.

Then *why* didn't you respond to him, or would you rather flame me
instead? I think we all know the answer to that.
So

>

[Oxyaena]

On 8/16/2018 7:09 AM, Peter Nyikos wrote:
[snip baseless insult]

Psychological projection noted.

>
> Yes, I do, and it isn't denial, fuckwad. I never insulted you in
> this post, but apparently you're all too willing to act like the
> immature sociopath you are rather than leave sbp out of the
> nonsense you conduct in talk.origins.
> https://groups.google.com/d/msg/sci.bio.paleontology/RNINuDOndSM/Yqpa_BOWBQAJ
>
> Wait, there's more from the same post:

I mean the post you initially replied to, which I will repost here in
its entirety:

"On 7/10/2018 3:00 PM, Peter Nyikos wrote:
> On Wednesday, June 27, 2018 at 8:57:34 AM UTC-4, John Harshman wrote:
>> On 6/26/18 6:35 PM, Peter Nyikos wrote:
>>> On Friday, June 22, 2018 at 1:14:40 AM UTC-4, John Harshman wrote:
>>>> On 6/21/18 7:04 PM, Peter Nyikos wrote:
>>>>> On Monday, June 18, 2018 at 9:21:03 PM UTC-4, John Harshman wrote:
>>>>>> On 6/18/18 5:42 PM, Peter Nyikos wrote:
>>>
>>>>>>> There are several examples of herbivores
>>>>>>> evolving into carnivores. The best known among mammals is
*Thylacoleo*,
>>>>>>> a Pleistocene marsupial from a suborder of almost exclusively
herbivores.
>>>>>>>
>>>>>>> There are also examples of herbivores evolving into opportunistic
>>>>>>> carnivores, like the well known black and brown rats. Such
marsupials
>>>>>>> include three related kangaroos, the Early to Middle Miocene
*Ekaltadeta*,
>>>>>>> the Early Pliocene *Jackmahoneya*, and the Pleistocene
*Propleopus*.
>>>>>>>
>>>>>>> These were the three known members of the subfamily *Propleopinae*
>>>>>>> when the following book, where this information can be found on
>>>>>>> pp. 151-153, as well as a fine exposition on *Thylacoleo* on
105-106:
>>>>>>>
>>>>>>> _Prehistoric Animals of Australia and New Zealand: One Hundred
>>>>>>> Million Years of Evolution_, by John Long, Michael Archer,
>>>>>>> Timothy Flannery, and Suzanne Head, The Johns Hopkins
University Press, 2002.
>>>>>>>
>>>>>>>
>>>>>>> As you may know, John Harshman
>>>>>>
>>>>>> /John Harshman/paleontologists/
>>>>>
>>>>> Which ones?
>>>>
>>>> Almost all, and most of the exceptions are aging out of the
population.
>>>
>>> And so the anti-ancestry-designation ideology continues to triumph.
>>> On grounds you've never been able to rationally articulate.
>>
>> We disagree on whether I've rationally articulated the grounds. Let me
>> try again. Let me start by noting that you are jumping around between
>> two separate issues: the acceptance of paraphyletic groups and the
>> assignment of particular fossil species as ancestors (or "ancestor
>> candidates). I (and most people who do classification and/or
>> phylogenetics) take exception to both of them, but they're different
things.
>>
>> Here, we're talking about the latter, "ancestor candidates". The main
>> objection to that practice is that we gain nothing by doing it.
>
> That is your private opinion. I think paleontologists in the field,
> trying to determine which fossils are potentially the most
> enlightening, would differ. And this applies also to paraphyletic
> taxa -- the closer the rank to species, the more valuable.
>

Actually, no. I happen to be married to a paleontologist and he accepts
the scientific consensus that Linnaean taxonomy is outdated, and that
cladistics is a far better method at explaining evolutionary
relationships than Linnaean taxonomy, which was designed in an era
before evolution.


>
>> All that
>> we can make use of is contained in the phylogenetic tree on which
>> ancestral nodes are not identified with real specimens.
>
> "real specimens" is confusing the issue; "accepted species" is
> where it is at. It would be sheer madness to claim that Equus
> evolved from the type specimen of Eohippus.

Of course it would be sheer madness, just as much it would be madness to
declare that humans are descended from Lucy, the holotype of
*Australopithecus afarensis*. Designating any fossil taxon, no matter
how intermediate in form they are, as the ancestor of anything alive
today is always unwise specifically because most fossils lack DNA, and
only in a very few cases can we definitively say that a fossil species
is the ancestor of something alive today, one of those rare cases is the
fact that *Homo heidelbergensis* is ancestral to both Neanderthals,
Denisovans, and modern humans.


>
> And no phylogenetic tree can hold a candle to pictures of
> skeletons of an ancestral candiate. Your computerized systematics
> does NOTHING for researchers in the field.

You wouldn't know, since you've never done any fieldwork.


>
>

>> It's from those
>> trees that we determine what ancestral states are, what transitions in
>> characters happened, even where and when those ancestors probably lived.
>> Designating ancestor candidates adds nothing to any of that.
>
> "any of that" is of use only to people who look at phylogenetic
> trees divorced from anatomy and fossils. But what do you
> expect from a theory of systematics which is increasingly based
> on EXTANT species?
>

I happen to agree with you on this, but I also agree with Harshman
insomuch that extinct taxa are tricky to handle when it comes to
systematics precisely because we don't have any DNA from them, and it's
a general rule of biology that molecular phylogenetics is far superior
to any cladogram derived from purely morphological data alone.



>>
>> Further, there is no way to confirm that the candidate really is an
>> ancestor, only that it sure resembles the inferred ancestor quite
closely.
>
> And that is very valuable information for people who cannot
> get really good information out of lists of hundreds of
> characters. You are falling prey to ye olde "forests for the trees"
problem.
>
> <small snip>
>
>>>>> Kathleen Hunt certainly did not embrace the reigning
>>>>> ideology when she wrote the FAQ on Equidae (actually Equioidea)
>>>>> for the Talk.Origins Archive. She really laid it on thick about
>>>>> various genera and even species being directly ancestral to others.
>>>>
>>>> Agreed, and she's an exception, assuming she's a paleontologist.
>>>
>>> I don't see how signififant that is: vertebrate paleontologists are
>>> a tiny minority of all systematists.
>>
>> I don't see your point. We were talking about paleontologists, weren't
>> we? We were talking about assigning fossils as ancestors, and the people
>> who would potentially do that are, for the most part, paleontologists.
>
> Yes, but they are hamstrung by a systematics that has less and
> less to do with them, dominated by non-paleontologists like yourself.

You don't know any actual paleontologists, do you?


>
>
>
>> There's very little opportunity to do such a thing unless you're dealing
>> with fossils. So paleontologists are the relevant people in this
>> particular discussion.
>>
>>>>> Kenneth V. Kardong departed from the reigning ideology in his
>>>>> 2012 standard text in vertebrate comparative anatomy and evolution,
>>>>> by devoting more space to the traditional Linnean classification
>>>>> than to the cladistic classification of vertebrates.
>>>>
>>>> Is he a paleontologist?
>>>
>>> I don't think so, but he is probably a comparative anatomist,
>>> which is at least as relevant to systematics.
>>
>> How is it "at least as relevant" as actually work on phylogeny and
>> classification? Almost every vertebrate paleontologist, incidentally, is
>> a systematist.
>
[snip idiocy]
>
>> Species descriptions, character states, and phylogenetic
>> trees are the meat of vertebrate paleo.
>
> No, just the bare bones. The real meat is being able to reconstruct
> actual species.
>>
>>>> Is what he did even an exception?
>>>
>>> I'd be very glad if it is not. It would mean that the your
>>> cladophilia does not permeate the anti-direct-ancestry leading
>>> ideology.
>>
>> Sorry, but I think you misunderstand the question. I don't mean to
>> question whether acceptance of paraphyletic groups is an outlier. We
>> were talking about paleontologists, and I question whether Kardong's
>> practice is relevant to the practice among paleontologists, or for that
>> matter to that of other systematists.
>>
>>> Cladophilia is my term for not tolerating the traditional
>>> Linnean classification within the science of systematics.
>>> You have consistently championed it in sci.bio.paleontology,
>>> and this is the first hint I have that cladophiles do not make up
>>> the overwhelming majority of systematists today.
>>
>> No such hint was intended or present.
>
> "Is what he did even an exception." How am I to interpret that,
> now that you have reverted to your old cladophile self?

You are the one who coined the term "cladophilia". Cladophilia doesn't

exist. Just because you have a problem with the current scientific

consensus doesn't mean jack shit in the long run. Are you actually
suggesting that you, a mere mathematician with no actual expertise on
this subject, knows far more about the issue of taxonomy than actual
specialists in the relevant fields? Sorry, Peter, but Harshman has you
beat on this.


>
>
>
>>> I am repeating a line from above because of the many lines in between:
>>>
>>>>>>> As you may know, John Harshman
>>>>>>> rejects as "unscientific, because
>>>>>>> subjective" any claim that either of the two earlier known
>>>>>>> members of *Propleopinae* are ancestral to the the third,
>>>>>>> or that the earliest is ancestral to the second.
>>>>>
>>>>> The above book has some information to suggest that the earliest
>>>>> genus in *Propleopinae* could be what I call a prime candidate
>>>>> for direct ancestry to either of the other two, and the second a
prime
>>>>> candidate for direct ancestry to the last.
>>>>
>>>> Does it? What would that information be, and why does it suggest what
>>>> you say?
>>>
>>> In many features in addition to size, *Jackamahoneya toxoniensis*
>>> is intermediate in morphology as well as age between the species
>>> of *Ekalatadeta* and those of *Propleopus*. [p. 151]
>>>
>>> Note, I said "suggests". One would have to do a very detailed study
>>> of the known fossils of these species in order to tell whether there is
>>> any prime candidate for direct ancestry between some pair of them.
>>
>> What you presumably mean is that one would have to code lots of
>> characters for all the species and perform a phylogenetic analysis,
>> since your criterion is identity with the inferred ancestor. Note that
>> the book itself makes no such claim, at least in what you've quoted
so far.
>>
>>>>> Do you remember my exacting standards for the concept of "prime
>>>>> candidate"? It risks missing out on a huge number of actual
>>>>> ancestries, but that is a price one must pay for challenging a
>>>>> deeply entrenched ideology.
>>>>
>>>> No, I don't remember. Remind me.
>>>
>>> No apomorphies that might rule out direct ancestry between two
>>> different vertebrates of which we have reasonably complete skeletons.
>>
>> Is that the sole criterion, or do you also add a stratigraphic one?
>
> Given the paucity of the fossil record, and apparent stasis in
> some lines for millions of years, stratigraphy plays a decisive
> role only in extreme cases.
>
>
>> So, in formal terms, you are saying that in a phlogenetic analysis, the
>> candidate is a taxon that's on a zero-length branch from the ancestral
>> node. As you point out, that's conservative in the sense that it might
>> eliminate some actual ancestors. But does it give us any confidence that
>> the candidate is an ancestor, and what can we usefully do with that
>> confidence?
>
> See above about researchers in the field. Adding more data to a
> reasonably complete specimen could either strengthen or falsify
> the "ancestor candidate" designation. That's the way science
> progresses, although bombast of "the debate is over" sort
> undermines that progress.
>
>
>>> I'm not conversant enough with non-vertebrate fossils to make any
>>> similar suggestions about them. There is a botanist who has a much
>>> less stringent criterion, but I don't know enough about botany
>>> to argue with him.
>>
>> Then let's keep this about vertebrates for now.
>>
>>>>>>> That's because he pronounces the same verdict on ANY purported
>>>>>>> example of an animal known only from fossils being ancestral
>>>>>>> to any other animal, whether extinct or extant. That includes all
>>>>>>> "subjective" talk about us being descended either from
>>>>>>> *Australopithecus* or *Ardipithecus*, or even from *Homo erectus*.
>>>>>>
>>>>>> This seems a gratuitous attack on a third party,
>>>>>
>>>>> It's not an attack at all; it's an acknowledgement of the hand
>>>>> anyone who challenges the reigning ideology has been dealt.
>>>>
>>>> You may be unconscious of the implications of your statements. You are
>>>> accusing me, personally, of being some kind of bigoted enforcer.
>>>
>>> Come off it. You have endorsed this very thing MANY times in the past,
>>> and it survives in your talk near the beginning about how
>>> the few paleontologists who do not share it are slowly dying off.
>>
>> Not sure what "this very thing" means. If it's "some kind of bigoted
>> enforcer", then I deny any such role.
>
> That's YOUR verbiage, and has nothing to do with "the few paleontologists
> who do not share it are slowly dying off."
>
>
>> I merely reflect and agree with
>> the common practice among the current scientific community.
>
> At one point, the current scientific community was even more
> certain that the sun revolved around the earth.

Logical fallacy of false equivocation. That scientific consensus was
derived from the data they had available at the time, as soon as new
evidence came about the paradigm shifted, as indeed it should be in
science. As new evidence came about that traditional Linnaean taxonomy
was insufficient in describing evolutionary relationships, and that a
new method, cladistics, far surpassed it in that area, the paradigm also
shifted.

Just because you have a problem with how the scientific consensus shifts
based on the available evidence doesn't mean that you're in the right,
and all of the experts are wrong. Indeed, that is how it should be, or
otherwise it wouldn't be science. Science is based off of the pursuit of
knowledge, and when new evidence comes about that overturns or modifies
old theories and hypotheses, those theories and hypotheses must be
revised or discarded in order to accommodate the new evidence, and the
scientific consensus shifts accordingly.
>
>
>>> You are reading all kinds of things into what I've written that aren't
>>> even suggested there, perhaps on account of that one word "verdict".
>>
>> "Verdict" is one relevant word, but the entire mention of me is
>> gratuitous and leans toward an attack on my character. If an attack
>> isn't what you intended, then never mind. But it's still a gratuitous
>> introduction of my name and supposed attitudes (supposed because I do
>> not actually object to the quote).
>
> You represent "the common practice among the current scientific
community"
> in s.b.p. Not invoking your name would naturally lead to the reaction,
> "what's this got to do with s.b.p."?
>
>
>>> I'll postpone dealing with the rest of your post to give you
>>> a chance to compare the beginning of this post to this end.
>>
>> If you didn't intend an attack on my character, I retract that claim.
>
> Thank you. No such attack was intended, as I hope I've made clear.
>
>
> Peter Nyikos
> Professor, Department of Maths -- standard disclaimer--

> University of South Carolina
> http://people.math.sc.edu/nyikos/"

Once again I've caught you in a self-serving lie.


>
[snip bullshit and personal attacks by Nyikos]

> [1] But there was one you said was on paleontology, but it
> was on evolution instead, band when I pointed this out,
> you came out with your non sequitur that was so weird,
> I told you that you need to get back on your meds.
>

Cladistics *isn't* paleontology, jackass. You're a hypocritical fuckwad.

>> on the
>> Pterosaur thread. Ignore when he does this, it only feeds the troll.
>
> I've been feeding the real troll -- yourself -- because you've
> been insisting that I feed you, on pain of being labeled a lying
> scumbag by yourself.

Psychological projection noted.

>
>
>>>
>>>> I had written:
>>>> By the way, you haven't responded to my post of yesterday
>>>> in reply to Ruben Safir, even though there was actual
>>>> paleontology at the end, not just systematics. Can you say "double
>>>> standard"?
>>>> --- from the Pterosaur thread to which you refer at the beginning
>
> Not only "double standard" but also "hypocrite" since you had
> been on my case for not replying to your posts on paleontology,
> and you keep demanding recognition for the "on-topic" posts you do.

Psychological projection and apparent double standards noted.

>
>>>> And the response was what you are reading above.
>

> Peter "King of Deceit" Nyikos
>

[Peter Nyikos]

On Thursday, August 16, 2018 at 1:57:51 PM UTC-4, Oxyaena wrote:
> On 8/16/2018 7:54 AM, Peter Nyikos wrote:
> [snip personal attacks and baseless accusations by Nyikos]

You are in deep denial over how thoroughly those accusations
were documented and reasoned.

Moreover, you are "forgetting" that you also
snipped some meaty paleontology by myself. In which I caught
you in an embarrassing error, to boot.

So much for your bragging about how important paleontology
is for you. Do you run your posts by your professional
paleontologist spouse to make sure that you don't make
any embarrassing mistakes? It sure doesn't look that way.


In short, you are just digging yourself in deeper, Thrinaxodon.

From now on, in s.b.p., I will address you as Thrinaxodon
until you get the counseling you need. As you know, if I were
to do that in talk.origins, my post would be censored.

The Thrinaxodon name lives so much in infamy in talk.origins
that the t.o. robo-moderator automatically rejects any post
where it is even mentioned. But the depth of your state of
denial, and your insane pack of lies over the last month,
have earned for you my use of it.

> > PS I was going to do an on-topic reply to Harshman first thing
> > this morning, then these two sickeningly self-serving posts
> > of yours caught my eye.
>
> Then *why* didn't you respond to him,

I plan to do that later today. And why are you concerned
about this? You haven't contributed one whit to the on-topic
discussion/debate I've been having with John.

Do you intend to start doing that, or is your 5+ year old,
self-initiated vendetta of more interest to you?

> or would you rather flame me
> instead?

It isn't an either/or situation, it is a both/and situation, coward.

> I think we all know the answer to that.

I am feeding the troll - yourself - at your insistence.
I gave the rationale for this in the first post I
did this morning.

Your mindless repetition of the taunt "Psychological
projection noted" in reply to this rationale
shows that the actual meaning of what I wrote
never sank in. That's yet another sign that you are
badly in need of counseling, and probably also of
expert psychiatric help.


Peter Nyikos

[John Harshman]

On 8/14/18 7:44 AM, Peter Nyikos wrote:

>> and in the process you alluded to an argument you might make for
>> paraphyletic taxa. Nothing much to talk about until you
>> actually make that argument.
>
> I read this to say: nothing much I, John, want to talk about until you,
> Peter, elaborate on some old arguments that Erik and I have seen you make
> many times. That is, unless you, Peter, say you don't want to
> elaborate on them, in which case I, John, will reluctantly
> use Carroll's pp11-12 as a proxy elaboration on some of them.
>
> Did I get that right?

Don't think so. But if you want to use Carroll pp11-12 as your
argument, I'll try it.

Page 11 offers no arguments, merely definitions of monophyly, holophyly,
and paraphyly. Page 12 likewise offers no argument, merely a description
of Hennig's artificial convention on species pseudoextinction. (That
last is a technical term; are you familiar with it?) Page 13, however,
does have an argument.

I don't find that argument either interesting or compelling.

Hennig's convention does *not* follow logically from the prohibition of
paraphyletic groups, for two reasons: 1) species are a special sort of
taxon that isn't defined by monophyly and 2) species are not placed at
internal nodes. Thus the question of species extinction at speciation
never actually arises.

Further, if speciation is asymmetrical — the "budding" that Mayr and
Gould talked about, called peripatric speciation — we can almost never
know that either.

To answer Carroll's question: yes, "Rhipidistian" fish must be
classified differently from extant clades, because there is no such
thing as "Rhipidistian"; it's a collection of different groups, some
more closely related to lungfish and others more closely related to
tetrapods. Carroll, on page 13, appears not to understand the idea of
nested groups. The existence of paraphyletic groups is not an inevitable
consequence of evolution; at least, if a fossil species is paraphyletic
we have no way to discern that, and we even have no good way to tell if
a fossil species actually is a biological species. Thus fossils are at
the tips of branches, because cladistic relationships are the only
things we can actually test.

[John Harshman]

On 8/14/18 7:44 AM, Peter Nyikos wrote:

>>> But I don't think ANY paleontologist lost any sleep over the fact
>>> that he was dealing in what is NOW called a "paraphyletic taxon."
>>> I've often posted to s.b.p. about how Romer, near the beginning
>>> of his classic _Vertebrate Paleontolgy_ (1945 edition) talked
>>> about "horizontal" and "vertical" subdivisions of a phylogenetic
>>> tree, and gave pros [1] and cons of each method.
>
> See my proactive elaboration on this below.

Turns out that Romer 1966 has what looks like the same discussion as
Romer 1945. But it actually says very little about pros and cons. What
it does say depends on our being able to identify ancestral species,
which we can't actually do. So even that little discussion is moot.

The vertical classification shown "makes clear the relation of early
ancestors to their descendants but separates them sharply from the
common ancestor and other side branches to which they are closely
related." On the other hand, the horizontal classification shown "unites
all the similar early forms into a common ancestral group but obscures
the relationship of [ancestral forms] to their descendants." Note,
first, that Romer uses "relationship" in two separate ways: similarity
in morphology or time and cladistic relationship. And he makes no
attempt to clarify definitions.

More importantly, note that Romer is fooling himself about the benefit
of horizontal classification. If the intent is to group similar forms,
no classification can do such a thing unless there are clear gaps in
morphology between groups. While this is often the case when considering
extant groups only, the addition of fossils means that, wherever a
dividing line is placed, it will separate similar forms and group them
with less similar forms. Any place you put the line between birds and
dinosaurs will separate two very similar fossils into different classes.
The goal of horizontal classification, then, is theoretically
impossible. Even if a convenient fossil gap exists, there is a strong
likelihood that it will be filled with new finds, as happened when all
the feathered theropods from China began to emerge.

>>> The "horizontal" explicitly produced paraphyletic taxa, [2] the
>>> "vertical" just as explicitly produced clades -- the only things
>>> that Harshman and Oxyaena (and, if she is telling the truth, her husband)
>>> will ever call "taxa".
>>>
>>> Over a century of systematics (when nobody thought there was
>>> anything the matter with horizontal subdivisions that produced
>>> paraphyletic taxa) shoved down the memory hole.
>>>
>>> [1] I'll gladly expound on the pros of the traditional classification,
>>> if you are willing to listen.
>>
>> Go for it.
>
> I was talking to Ruben, not you. Hence my comment about your use of
> "we" up there.

Why are you willing to talk to Ruben but not to me?

>>> [2] It has to be done the way Romer illustrated it, to avoid
>>> polyphyletic taxa. Those were pretty well purged from the formal
>>> classification, with the exception of Holostei, whose polyphyletic
>>> nature was explicitly acknowledged by Romer [yes, he used the
>>> word "polyphyletic"].
>>
>> I don't have the 1945 edition, just 1966. Are these illustrations the same?
>>
> I have never seen the 1966 edition,
> so I can't answer your question.

Based on your description, they are the same, and I think the
accompanying text is too.

> On p. 6 of the 1946 edition, there is a Fig. 1 which shows the same
> small evolutionary tree cut up two different ways, the "vertical"
> (cladistic, except for having actual genera/species at the nodes)
> and the "horizontal" (showing a paraphyletic ancestral taxon, Family C).
> It tells the pros and cons of each, and uses the words "closely related"
> in a way antithetical to the cladophile-serving way: the way people
> use the term in everyday life.
>
> Can you find it in your 1966 edition?

Yes. Actually, it uses "related" in both the cladistic and the
temporal/morphological senses, and points out that to recognize one is
to obscure the other. The lesson I (though not Romer) take from that is
that there must be a unitary principle of classification, because
attempting a hybrid of two principles results only in confusion. Thus
phylogeny should be our guide.

>>>> There
>>>> are no reptiles. We have Archosaurs, Squamata, Synapsida, Mammals,
>>>> Aves, Dinasoria, Testudinata..
>>>
>>> Your use of lower case "reptiles" makes this a fallacious pastiche of formal
>>> and everyday usage.
>>>
>>>
>>>> Turles, Snakes and Crocs are less related to each other than Birds and
>>>> Crocs..
>>>>
>>>> What an amazing discovery.
>>>
>>> Done, and taken in its stride, before any of us was born.
>
> With, of course, the cladophile-serving use of the words "less related".

Is it your claim that turtles, snakes, and crocs are not less related to
each other than birds and crocs? I'd like to see you defend that claim,
if so.

[Oxyaena]

On 8/16/2018 3:20 PM, Peter Nyikos wrote:
> On Thursday, August 16, 2018 at 1:57:51 PM UTC-4, Oxyaena wrote:
>> On 8/16/2018 7:54 AM, Peter Nyikos wrote:
>> [snip personal attacks and baseless accusations by Nyikos]
>
> You are in deep denial over how thoroughly those accusations
> were documented and reasoned.

Bullshit. I need documentation. Put up or shut up, neither of which
you're seemingly capable of doing.

>
> Moreover, you are "forgetting" that you also
> snipped some meaty paleontology by myself. In which I caught
> you in an embarrassing error, to boot.

What paleontology, and what "error"? You're pulling things out of thin
air. Can you see things others can't?

>
> So much for your bragging about how important paleontology
> is for you. Do you run your posts by your professional
> paleontologist spouse to make sure that you don't make
> any embarrassing mistakes? It sure doesn't look that way.

I'm also a paleontologist, asshole. Specify what this supposed
"embarrassing mistake" was. You're delusional, and you need help.

>
>
> In short, you are just digging yourself in deeper, Thrinaxodon.

Why are you deliberately trying to provoke me, again? You *know* that
calling me Thrinaxodon is a way of trying to piss me off, so why do it?
Is it because you're *that* much of a douche bag? I believe so.

>
> From now on, in s.b.p., I will address you as Thrinaxodon
> until you get the counseling you need. As you know, if I were
> to do that in talk.origins, my post would be censored.

Go fuck yourself, you self-righteous prick. I need no counseling, and
you are the last person on earth to advise others to go see counseling.

>
> The Thrinaxodon name lives so much in infamy in talk.origins
> that the t.o. robo-moderator automatically rejects any post
> where it is even mentioned. But the depth of your state of
> denial, and your insane pack of lies over the last month,
> have earned for you my use of it.

Baseless insults noted. You need help, insult addict, you need *serious*
help.

>
>
>>> PS I was going to do an on-topic reply to Harshman first thing
>>> this morning, then these two sickeningly self-serving posts
>>> of yours caught my eye.
>>
>> Then *why* didn't you respond to him,
>
> I plan to do that later today. And why are you concerned
> about this? You haven't contributed one whit to the on-topic
> discussion/debate I've been having with John.

*None* of it is on-topic. Cladistics *isn't* paleontology, asshole.

>
> Do you intend to start doing that, or is your 5+ year old,
> self-initiated vendetta of more interest to you?

YOU initiated this so-called vendetta, coward. The first time I posted
to t.o. I noticed your trolling and spamming with your virulently
off-topic "Witch hunt on talk.origins" thread, and I asked why you were
such an asshole. You responded with your usually patronizing way
whenever you see a new poster, and that immediately ticked me off to the
fact that you were a condescending asshole.

>
>
>> or would you rather flame me
>> instead?
>
> It isn't an either/or situation, it is a both/and situation, coward.

Insult noted. BTW, you tacitly admitted to flaming me here. Perhaps you
should brush up on your ability to play verbal acrobatics.

>
>
>> I think we all know the answer to that.
>
> I am feeding the troll - yourself - at your insistence.
> I gave the rationale for this in the first post I
> did this morning.

I think it's the other way around, asshole.

>
> Your mindless repetition of the taunt "Psychological
> projection noted" in reply to this rationale
> shows that the actual meaning of what I wrote
> never sank in. That's yet another sign that you are
> badly in need of counseling, and probably also of
> expert psychiatric help.

Psychological projection noted, and the expert practice of Internet
Psychiatry. Is it any wonder that your students hate you?

>
>
> Peter Nyikos
>

[John Harshman]

Please, could both of you stop this? I don't read either side of this
mutual harangue. It just clutters up the group.

[Peter Nyikos]

On Thursday, August 16, 2018 at 12:15:55 PM UTC-4, John Harshman wrote:
> On 8/15/18 6:26 PM, Peter Nyikos wrote:
> > On Wednesday, August 15, 2018 at 9:49:37 AM UTC-4, John Harshman wrote:
> >> On 8/15/18 4:17 AM, Peter Nyikos wrote:
> >>
> >>> Huh? Wasn't paleontology just swept away in the flood of
> >>> "the cladistic wars," carried on mostly by systematists
> >>> who were, at best, amateur paleontologists (and that in the minority
> >>> of cases)?
> >>
> >> No. The cladist wars hit different fields at different times, and the
> >> battles were all internal to those fields.
> >
> > Thank you for this information.
> >
> >> Your acquaintance with the
> >> events is apparently minimal and is probably colored by your desire that
> >> the outcome be illegitimate.
> >
> > Only the ideological part.
> >
> > As for the scientific part, I keep reading bits and pieces about
> > the "cow - lungfish - salmon" debate, but from what I've read,
> > the traditional systematists picked a lousy third taxon. They
> > could have done a lot better to pick the bichir *Polypterus*
> > for that third taxon.
>
> Why?

Actually, when the debate was among systematists where the majority
were only researching extant species, the best choice was the
coelacanth *Latimeria*.

OTOH among paleontologists, the best strategy might have been to replace
all but the first:
{cow, *Elginerpeton*, *Tiktaalik*}

Can you see why? Before you answer, please take a look at the cladogram
at the bottom of:

https://en.wikipedia.org/wiki/Stegocephalia

> And what have you been reading?

Little bits and pieces over the years. I can only remember one
of them, and I can look it up if you are interested, but I am
short on time at the moment.

What have YOU read about this supposedly famous debate about
the trio that they used?

> > Worse yet, they either did not know how Romer 1945 used the term
> > "closely related " in a completely different way than the
> > way I've seen it used in every account I've seen so far,
> > or else we have another example of "history is written by the victors."
> >
> > That reminds me: did you see whether the 1966 edition has something
> > fitting the description I gave you of Fig. 1 of the 1945 edition
> > in a post of yesterday? You haven't replied to that post yet.
>
> Yes, I saw it, and I suspect the text didn't change either. To the
> extent Romer's text contains an argument for paraphyly, that argument is
> seriously flawed.

I see you are tenaciously clinging to your lack of support for
"no, no, no, and no," and even for provocative comments like
the one you've just made, which would at least initiate a support
for one or more "no"s.

On the other hand, I begin to support a Yes answer to 2. later
in this post.

> Ironically, the inclusion of fossils makes it more
> flawed than if he had considered only extant species.

I think the opposite is true, and I'll explain in detail when
I have more time to spare. Meanwhile, your tenacious clinging
to your policy is exacerbated by the leading word "Ironically."

> >>> Don't worry, I'll start supporting Yes answers before the week is out,
> >>
> >> Excellent.

Do you also think it is excellent for you to make unsupported
provocative statements in counterfeit support of your "no"s?

> >>> John had nothing to say about Hennig's convention, and I suppose you
> >>> don't either.
> >>
> >> Hennig's convention is irrelevant to cladistic classification,
> >> paraphyletic groups, etc.
> >
> > What do you mean? As Carroll points out on p. 13, the result of
> > this convention is that almost exactly half of all species that
> > ever existed were paraphyletic.
> >
> > Another offshoot of this convention is to use the term "hypothetical"
> > for all of them, as though that made them somehow outside the field
> > of science, and safely "out of sight [except for all those pesky
> > nodes], out of mind".
>
> I am unable to interpret that statement. But no, the hypothetical nature
> of internal nodes has nothing at all to do with Hennig's convention, so
> perhaps I don't have to understand your attempted point. The reason
> internal nodes are hypothetical is that we can't assign actual species
> to them,

Yes, but not for any reason given in previous discussions.

The main reason is that assigning species to them would result in
massive distortions of evolutionary history in a way inevitable
as long as the Hennig extinction convention is used. This is brought out
in the examples I gave below.

> and thus we avoid making claims that can't be supported by the
> data. What we can make claims about would be the character states at
> those nodes,

I suppose the distinction between (a) different characters and
(b) different states of one character
is made by decisions about what is homologous to what.
We cannot very well have paraphyletic characters, now, can we?

> which can be turned into a description of that unknown
> ancestor. Of course that description is an estimate, as everything in
> science.

Including "ancestor candidate," but you are against accepting
that in science, aren't you?

> >> It's irrelevant because of two things: 1)
> >> species are not generally defined by monophyly but by propensity to
> >> interbreed, which is plesiomorphic,
> >
> > I fail to see the relevance, unless you are referring to the convention
> > that no named species should ever have been subject to speciation.
> > And that segues into my reply to your next point.
>
> There is no such convention, so again I can't interpret that statement.
> The relevance is that species are a special sort of taxon. All other
> taxa are defined as clades, but species are not.

Why didn't you express yourself this clearly before, instead of
using all that technical language?

>
> There is also a problem with defining species when you extend them over
> space and time. Regarding space, consider ring species. And the same
> sort of gradual transition resulting in discontinuity, over time rather
> than space, is much more common.

Yes, but those are small perturbations, not to be compared to the
possible major distortions explained below.

> >> and, more importantly, 2) we can't
> >> identify ancestors in the fossil record, and the convention relies on
> >> placing actual taxa at internal nodes.
> >
> > The irony is that, say, a clade of 8 species would have 7 or 8 paraphyletic
> > species hidden away in the nodes by the convention, while there
> > might in reality be only one paraphyletic species involved, and
> > be mistaken for one of the "actual taxa" because it is still alive.
>
> I don't understand that either,

Why not? Granted, that "because" is misleading. ANY recognized
species would be treated in exactly that way.

Are you, a professional systematist, unable to visualize what
I had in mind? One species forming a "limb" and all the others
branches sprouting from its side. The species then stands
at the apex of the limb, treated by cladists in the same way
as those side branches.

And your next statement is irrelevant, because all phylogenetic
trees work that way, convention or no convention.

And here is my first support of a Yes answer to:

2. Should particular fossil "species" be declared to be ancestors or
ancestor candidates, and if so, what is gained?

What is gained is a diminution of these distortions of actual
evolutionary history, as has already been done for Equioidea to a great
extent in Kathleen Hunt's evolutionary (not phylogenetic)
tree. Yes, some of those ancestor-descendant relationships
may later be falsified, but replaced by a better candidate.

One example: for a long time, it was thought that Equus
descended from Pliohippus, but when Dinohippus was shown
to be a better candidate because its molars were less
curved, it replaced Pliohippus; and this is explained in
Kathleen Hunt's horse family FAQ.

> but since nobody is defending that silly
> convention there seems no point.

Where did you even hint, before here, that this particular convention by
Hennig was silly? And is your opinion your own, or is it the "consensus"
of systematists?

> > And you call yourselves "objective" and "scientific" while denying
> > those terms to traditional systematists!
>
> Yes. I don't understand what argument you are making that cladistic
> classification isn't objective or scientific, or perhaps that
> traditional classification is either.
>
> I exhort you to greater effort to make your arguments clear.

I think this means: "I exhort you to start making statements that
don't rub me the wrong way."

> Now much of
> my current confusion may have to do with your proceeding from false
> premises, but I don't think all of it is.

I don't think any of it is. And I'd like to see even one example
of what you might think to be a false premise behind ANYTHING
I've said, whether conducive to confusion in your mind, or not.

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

PS I still haven't replied to the post of yours that I've been
hoping to reply to for two days, and it may even have to wait
until tomorrow, but at least this one is more than a whole
day before the (work) week is out.

[Oxyaena]

Why? Unlike extant organisms, most fossils lack DNA, and therefore the
only means left for us to classify them is morphology, and we all know
how inaccurate morphologically based phylogenies can get.

>
>>>>> Don't worry, I'll start supporting Yes answers before the week is out,
>>>>
>>>> Excellent.
>
> Do you also think it is excellent for you to make unsupported
> provocative statements in counterfeit support of your "no"s?

Your usage of the term "counterfeit" implies that Harshman is being
dishonest, when he is in fact not, and I suggest you refrain from
insults when they clearly aren't necessary.

Here is something many of us have asked, but something you have *never*
answered: Why do *you* prefer paraphyly and Linnaean taxonomy over
cladistics? *Why* do you think Linnaean taxonomy is preferable to
cladistics? Are you even *capable* of answering those questions?

How many times do I have to explain to you that the scientific consensus
is based off of the evidence available at hand, not what people prefer,
and the evidence indicates cladistics shows evolutionary relationships
more accurately than Linnaean taxonomy does. For example, you proposed
that under Linnaean taxonomy *Steropodon* and other monotremes would be
placed inside their own suborder of Monotremata, even though
*Steropodon* is more closely related to platypuses than to echidnas, and
I retorted that would give the false impression that Mesozoic monotremes
were a single monophyletic clade, and their descendants an entirely
different clade, arbitrarily distinguished from each other when there
was no such distinguishing basis in actuality. You usually ignore when I
bring this up because it inconveniences you, and I suspect you will do
so here, or dishonestly snip it, whichever one suits you best.

>
>
>>> And you call yourselves "objective" and "scientific" while denying
>>> those terms to traditional systematists!
>>
>> Yes. I don't understand what argument you are making that cladistic
>> classification isn't objective or scientific, or perhaps that
>> traditional classification is either.
>>
>> I exhort you to greater effort to make your arguments clear.
>
> I think this means: "I exhort you to start making statements that
> don't rub me the wrong way."

So you willingly refuse to *not* be a dick? Not surprised.

>
>
>> Now much of
>> my current confusion may have to do with your proceeding from false
>> premises, but I don't think all of it is.
>
> I don't think any of it is. And I'd like to see even one example
> of what you might think to be a false premise behind ANYTHING
> I've said, whether conducive to confusion in your mind, or not.

Look up the PhyloCode, nitwit, and see what he means by "false premises".

>
>
> Peter Nyikos
> Professor, Dept. of Mathematics -- standard disclaimer--
> University of South Carolina
> http://people.math.sc.edu/nyikos/
>
> PS I still haven't replied to the post of yours that I've been
> hoping to reply to for two days, and it may even have to wait
> until tomorrow, but at least this one is more than a whole
> day before the (work) week is out.
>

Translation: "I'll get to it when I feel like it, even if it's two
months from now."

[Oxyaena]

On 8/15/2018 5:57 PM, Peter Nyikos wrote:
> On Wednesday, August 15, 2018 at 8:38:16 AM UTC-4, Oxyaena wrote:
>> On 8/15/2018 7:40 AM, Peter Nyikos wrote:
>>> On Wednesday, August 15, 2018 at 7:19:24 AM UTC-4, Oxyaena wrote:
>>>> On 8/15/2018 7:17 AM, Peter Nyikos wrote:
>>>>
>>>> Why are you wasting everyone's time ranting about your pet peeves
>>>> against cladistics, when you could actually be doing something
>>>> constructive like responding to the posts about paleontology I just put up?
>
> "posts" is plural, yet the one you "just (now)" had put up when you
> said this was not about paleontology at all, while the one before that
> was a specialized one on Felidae that I don't have anything to add to.
>

Then what about the one on creodonts, or pterosaurs, or extinction
ratios of the K-Pg extinction event? None of those you've responded to.
I responded to you on the *Oreopithecus* thread long ago and you never
got around to responding to me. Why?

>>>
>>> Because the "indignant" replies to me that you keep making on this thread,
>>> and on the "Pterosaur dietary hypotheses" thread, seem to mean
>>> far more to you than either paleontology or cladistics.
>>>
>>> Peter Nyikos
>>>
>
> You do not deny that they mean far more to you, but jump to a weird
> conclusion instead.
>
>> So you admit you don't give a shit about actually disucssing on-topic
>> material and would rather flame me? Not surprised.
>
> You were proudly touting YOUR posts, and that's ALL I was referring to.
>
> And this whole thread is primarily on cladistic vs traditional classification
> methods, and I have been discussing them with Harshman. You are strangely absent from that discussion.
>

Because I have no need to, I'd much rather discuss on-topic paleontology
rather than the debate between cladistics and Linnaean taxonomy. You
berate me for posting something on evolution here, but you conveniently
forget that sbe is dead and the posters in talk.origins aren't as
interested in the subjects we post about here, even though it would be
ostensibly on-topic over there. I think the implied reason why you
berate me is so you can score another point against me in this vendetta
of yours, since you've *never* berated Ruben for posting off-topic posts
here, such as those mutation rates, and even berated me for doing so,
you hypocrite.

[John Harshman]

Once again, why? What are you talking about?

> OTOH among paleontologists, the best strategy might have been to replace
> all but the first:
> {cow, *Elginerpeton*, *Tiktaalik*}

?

> Can you see why? Before you answer, please take a look at the cladogram
> at the bottom of:
>
> https://en.wikipedia.org/wiki/Stegocephalia
>
>
>> And what have you been reading?
>
> Little bits and pieces over the years. I can only remember one
> of them, and I can look it up if you are interested, but I am
> short on time at the moment.
>
> What have YOU read about this supposedly famous debate about
> the trio that they used?

I don't have any idea what you're talking about, so I appear not to have
read anything. What are you talking about?

>>> Worse yet, they either did not know how Romer 1945 used the term
>>> "closely related " in a completely different way than the
>>> way I've seen it used in every account I've seen so far,
>>> or else we have another example of "history is written by the victors."
>>>
>>> That reminds me: did you see whether the 1966 edition has something
>>> fitting the description I gave you of Fig. 1 of the 1945 edition
>>> in a post of yesterday? You haven't replied to that post yet.
>>
>> Yes, I saw it, and I suspect the text didn't change either. To the
>> extent Romer's text contains an argument for paraphyly, that argument is
>> seriously flawed.
>
> I see you are tenaciously clinging to your lack of support for
> "no, no, no, and no," and even for provocative comments like
> the one you've just made, which would at least initiate a support
> for one or more "no"s.
>
> On the other hand, I begin to support a Yes answer to 2. later
> in this post.

All these side comments and characterizations are getting in the way of
any real discussion. Please stop.

>> Ironically, the inclusion of fossils makes it more
>> flawed than if he had considered only extant species.
>
> I think the opposite is true, and I'll explain in detail when
> I have more time to spare. Meanwhile, your tenacious clinging
> to your policy is exacerbated by the leading word "Ironically."

Please stop the empty characterizations. A more reasonable approach
would have been to ask me to explain.

>>>>> Don't worry, I'll start supporting Yes answers before the week is out,
>>>>
>>>> Excellent.
>
> Do you also think it is excellent for you to make unsupported
> provocative statements in counterfeit support of your "no"s?

I will no longer reply to this sort of thing. Please stop.

>>>>> John had nothing to say about Hennig's convention, and I suppose you
>>>>> don't either.
>>>>
>>>> Hennig's convention is irrelevant to cladistic classification,
>>>> paraphyletic groups, etc.
>>>
>>> What do you mean? As Carroll points out on p. 13, the result of
>>> this convention is that almost exactly half of all species that
>>> ever existed were paraphyletic.
>>>
>>> Another offshoot of this convention is to use the term "hypothetical"
>>> for all of them, as though that made them somehow outside the field
>>> of science, and safely "out of sight [except for all those pesky
>>> nodes], out of mind".
>>
>> I am unable to interpret that statement. But no, the hypothetical nature
>> of internal nodes has nothing at all to do with Hennig's convention, so
>> perhaps I don't have to understand your attempted point. The reason
>> internal nodes are hypothetical is that we can't assign actual species
>> to them,
>
> Yes, but not for any reason given in previous discussions.
>
> The main reason is that assigning species to them would result in
> massive distortions of evolutionary history in a way inevitable
> as long as the Hennig extinction convention is used. This is brought out
> in the examples I gave below.

You are incorrect. The reason species are not assigned to internal nodes
is that we can't identify ancestors.

>> and thus we avoid making claims that can't be supported by the
>> data. What we can make claims about would be the character states at
>> those nodes,
>
> I suppose the distinction between (a) different characters and
> (b) different states of one character
> is made by decisions about what is homologous to what.
> We cannot very well have paraphyletic characters, now, can we?

I am unable to make sense of that. What would a paraphyletic character
even mean?

>> which can be turned into a description of that unknown
>> ancestor. Of course that description is an estimate, as everything in
>> science.
>
> Including "ancestor candidate," but you are against accepting
> that in science, aren't you?

Yes. We gain nothing by talking about ancestor candidates.

>>>> It's irrelevant because of two things: 1)
>>>> species are not generally defined by monophyly but by propensity to
>>>> interbreed, which is plesiomorphic,
>>>
>>> I fail to see the relevance, unless you are referring to the convention
>>> that no named species should ever have been subject to speciation.
>>> And that segues into my reply to your next point.
>>
>> There is no such convention, so again I can't interpret that statement.
>> The relevance is that species are a special sort of taxon. All other
>> taxa are defined as clades, but species are not.
>
> Why didn't you express yourself this clearly before, instead of
> using all that technical language?

So do you agree that there is no such convention?

>> There is also a problem with defining species when you extend them over
>> space and time. Regarding space, consider ring species. And the same
>> sort of gradual transition resulting in discontinuity, over time rather
>> than space, is much more common.
>
> Yes, but those are small perturbations, not to be compared to the
> possible major distortions explained below.

I would consider it to be a major problem in relating fossil "species"
to the biological species concept.

>>>> and, more importantly, 2) we can't
>>>> identify ancestors in the fossil record, and the convention relies on
>>>> placing actual taxa at internal nodes.
>>>
>>> The irony is that, say, a clade of 8 species would have 7 or 8 paraphyletic
>>> species hidden away in the nodes by the convention, while there
>>> might in reality be only one paraphyletic species involved, and
>>> be mistaken for one of the "actual taxa" because it is still alive.
>>
>> I don't understand that either,
>
> Why not? Granted, that "because" is misleading. ANY recognized
> species would be treated in exactly that way.

In exactly what way? I really have no idea what you're talking about
here. Again, there is no such convention, so anything you say assuming
there is makes little sense.

> Are you, a professional systematist, unable to visualize what
> I had in mind? One species forming a "limb" and all the others
> branches sprouting from its side. The species then stands
> at the apex of the limb, treated by cladists in the same way
> as those side branches.

Sure. What's the problem? But you're wrong. If you're talking about a
paleontological "species" that lasted for many millions of years but is
considered morphologically conserved over that time, what a cladogram
would probably show would be a complete polytomy. The ancestral species
would have zero apomorphies, while each descendant species would have
its own autapomorphies, with no characters able to prodice a tree structure.

But this all relies on using a morphological species concept, not the
biological species concept.

> And your next statement is irrelevant, because all phylogenetic
> trees work that way, convention or no convention.

What way? Once again, there is no such convention.

> And here is my first support of a Yes answer to:
>
> 2. Should particular fossil "species" be declared to be ancestors or
> ancestor candidates, and if so, what is gained?
>
> What is gained is a diminution of these distortions of actual
> evolutionary history, as has already been done for Equioidea to a great
> extent in Kathleen Hunt's evolutionary (not phylogenetic)
> tree. Yes, some of those ancestor-descendant relationships
> may later be falsified, but replaced by a better candidate.

But this goes nowhere. There is no science that can then be done using
the assumption, even a tentative one, that this species is the ancestor.
Nothing that couldn't be done without such an assumption.

And this is not a distortion, merely an admission of the limits of our
knowledge.

> One example: for a long time, it was thought that Equus
> descended from Pliohippus, but when Dinohippus was shown
> to be a better candidate because its molars were less
> curved, it replaced Pliohippus; and this is explained in
> Kathleen Hunt's horse family FAQ.

So? What good was declaring Piohippus to be an ancestor candidate, or by
replacing it with Dinohippus, other than fixing the tree, which could
have been done without declaring ancestors?

>> but since nobody is defending that silly
>> convention there seems no point.
>
> Where did you even hint, before here, that this particular convention by
> Hennig was silly? And is your opinion your own, or is it the "consensus"
> of systematists?

I don't recall the subject ever coming up before, and nobody that I know
of ever uses this convention; again, since it's impossible to recognize
ancestors the question never comes up.

>>> And you call yourselves "objective" and "scientific" while denying
>>> those terms to traditional systematists!
>>
>> Yes. I don't understand what argument you are making that cladistic
>> classification isn't objective or scientific, or perhaps that
>> traditional classification is either.
>>
>> I exhort you to greater effort to make your arguments clear.
>
> I think this means: "I exhort you to start making statements that
> don't rub me the wrong way."

No. Assume that when I say I don't understand, that's an actual
statement that I don't understand and an opportunity for you to clarify.

>> Now much of
>> my current confusion may have to do with your proceeding from false
>> premises, but I don't think all of it is.
>
> I don't think any of it is. And I'd like to see even one example
> of what you might think to be a false premise behind ANYTHING
> I've said, whether conducive to confusion in your mind, or not.

The belief that there's a common convention that species become extinct
upon speciation and that no species is paraphyletic. A mistaken notion
of what a paraphyletic species would look like on a tree. And the notion
that declaring ancestor candidates gains something of value to science.

[Peter Nyikos]

Finally, I get a halfway sincere and sane, and almost wholly on-topic,
reply from Oxyaena!

This will help me to decide just how to handle the request
John made to both of us in a reply to Oxyaena (mild surprise: not
to me).

Have YOU read anything about it, Oxyaena?

> >
> >>> Worse yet, they either did not know how Romer 1945 used the term
> >>> "closely related " in a completely different way than the
> >>> way I've seen it used in every account I've seen so far,
> >>> or else we have another example of "history is written by the victors."
> >>>
> >>> That reminds me: did you see whether the 1966 edition has something
> >>> fitting the description I gave you of Fig. 1 of the 1945 edition
> >>> in a post of yesterday? You haven't replied to that post yet.
> >>
> >> Yes, I saw it, and I suspect the text didn't change either. To the
> >> extent Romer's text contains an argument for paraphyly, that argument is
> >> seriously flawed.
> >
> > I see you are tenaciously clinging to your lack of support for
> > "no, no, no, and no," and even for provocative comments like
> > the one you've just made, which would at least initiate a support
> > for one or more "no"s.
> >
> > On the other hand, I begin to support a Yes answer to 2. later
> > in this post.
> >
> >
> >> Ironically, the inclusion of fossils makes it more
> >> flawed than if he had considered only extant species.
> >
> > I think the opposite is true, and I'll explain in detail when
> > I have more time to spare. Meanwhile, your tenacious clinging
> > to your policy is exacerbated by the leading word "Ironically."
> >
>
> Why?

I take it you haven't seen the evolutionary tree in Romer's text.

It is a tree which can be very well applied to perissodactyls,
as suggested by Romer. I will use this very appropriate example.

Branching off from a common ancestral form C are Family A and
Family B. Romer suggests horses for A and rhinoceroses for B
as a concrete example, and I'll go with that.

At the base of Family A is genus A' (say, Eohippus, now "known" to be
distinct from Hyracotherium according to ungulate specialist Donald Prothero)
and at the base of Family B is genus B' (say, Hyrachyus). Both
are quite close to their LCA, genus C.

Then family A has two successive nodes marked with taxa (say,
Mesohippus and Miohippus) before it branches off two ways
(say, towards Hypohippus and Equus), with
another intermediate species on the latter branch (say Merychippus)
before it branches off again.

Family B also has two genera before it splits into two branches,
but neither branch bifurcates after that.

Romer also has a branch from C to a form D, just before the last
known ancestral forms A' and B' of the two families. To show how
John's "Ironically..." was uninformed by what he saw, let D
be Hyracotherium, which according to Prothero was actually
an early Palaeothere.

Romer says A' and B' are "closely related" to D, but the
vertical (cladistic) classification puts them in different
families from each other and from D.

Anyone who understands why siblings are more closely related than
one of them is to his/her great-great-great grandchild, can readily
understand this "heretical" use of the term "closely related."

That's why I want to get to the bottom of what happened during
the "cladist wars". I find it very hard to believe that none
of the traditional systematists didn't press the issue of
Romer's usage, and adopt it for their own.

And in what sense was that particular "cladist war" (or set
of cladist wars) won by the cladists. Was it put to a democratic
or oligarchial vote, for example? Under "oligarchial" I include
basing it on the vote of people registered for and present at a national
conference.

Many of the most important decisions of the American Mathematical
Society are oligarcial in this respect.

> Unlike extant organisms, most fossils lack DNA, and therefore the
> only means left for us to classify them is morphology, and we all know
> how inaccurate morphologically based phylogenies can get.

That's why I chose the illustrative example I did. The point is,
how do you split the tree up into groups, once it is decided on?

> >>>>> Don't worry, I'll start supporting Yes answers before the week is out,
> >>>>
> >>>> Excellent.
> >
> > Do you also think it is excellent for you to make unsupported
> > provocative statements in counterfeit support of your "no"s?

> Your usage of the term "counterfeit" implies that Harshman is being
> dishonest,

No, he may just be innocently passing on counterfeit "support."
It was only recently that I learned that the pejorative "unnatural"
for paraphyletic taxa was not original with him, but had been used
long ago by C. Patterson.

Is the term "disease" something you were uncritically repeating from
a "research" article like the one by C. Patterson?

> when he is in fact not, and I suggest you refrain from
> insults when they clearly aren't necessary.

...glass houses...stones. Look at your parting insult at the end.

I wasn't insulting him, I was characterizing the use of a bald
assertion to support another bald assertion of "no" to one
or more of the four questions on the OP.

>
> >
> >>>>> John had nothing to say about Hennig's convention, and I suppose you
> >>>>> don't either.
> >>>>
> >>>> Hennig's convention is irrelevant to cladistic classification,
> >>>> paraphyletic groups, etc.
> >>>
> >>> What do you mean? As Carroll points out on p. 13, the result of
> >>> this convention is that almost exactly half of all species that
> >>> ever existed were paraphyletic.
> >>>
> >>> Another offshoot of this convention is to use the term "hypothetical"
> >>> for all of them, as though that made them somehow outside the field
> >>> of science, and safely "out of sight [except for all those pesky
> >>> nodes], out of mind".
> >>
> >> I am unable to interpret that statement.

Are YOU able to interpret it? If not, what is it about it that
you don't understand?

> > > But no, the hypothetical nature
> >> of internal nodes has nothing at all to do with Hennig's convention, so
> >> perhaps I don't have to understand your attempted point. The reason
> >> internal nodes are hypothetical is that we can't assign actual species
> >> to them,
> >
> > Yes, but not for any reason given in previous discussions.
> >
> > The main reason is that assigning species to them would result in
> > massive distortions of evolutionary history in a way inevitable
> > as long as the Hennig extinction convention is used. This is brought out
> > in the examples I gave below.
> >
> >
> >> and thus we avoid making claims that can't be supported by the
> >> data. What we can make claims about would be the character states at
> >> those nodes,
> >
> > I suppose the distinction between (a) different characters and
> > (b) different states of one character
> > is made by decisions about what is homologous to what.
> > We cannot very well have paraphyletic characters, now, can we?
> >
>
> Here is something many of us have asked, but something you have *never*
> answered:

Actually, I think you are the only one who has asked it since 2001.

> Why do *you* prefer paraphyly and Linnaean taxonomy over
> cladistics?

I don't, and I've made that clear many times, including my direct
answer to Harshman's OP. Why didn't you read it?

> *Why* do you think Linnaean taxonomy is preferable to
> cladistics? Are you even *capable* of answering those questions?

This is one reason I wrote "halfway" before "sincere and sane." AT BEST,
you are baselessly guessing false "facts" about me. At worst...
well, if you are halfway sane, you can correctly guess what
those ellipses are shorthand for.

>
> >
> >> which can be turned into a description of that unknown
> >> ancestor. Of course that description is an estimate, as everything in
> >> science.
> >
> > Including "ancestor candidate," but you are against accepting
> > that in science, aren't you?

Same question to you, Oxyaena.

> >>>> It's irrelevant because of two things: 1)
> >>>> species are not generally defined by monophyly but by propensity to
> >>>> interbreed, which is plesiomorphic,
> >>>
> >>> I fail to see the relevance, unless you are referring to the convention
> >>> that no named species should ever have been subject to speciation.
> >>> And that segues into my reply to your next point.

<snip for focus>

Did you read these two paragraphs, or did you decide not to catch the
"cladophobe" "disease" from me after a hasty skim, and to quickly
move on?

> >> but since nobody is defending that silly
> >> convention there seems no point.
> >
> > Where did you even hint, before here, that this particular convention by
> > Hennig was silly? And is your opinion your own, or is it the "consensus"
> > of systematists?
>
> How many times do I have to explain to you that the scientific consensus
> is based off of the evidence available at hand,

The term "scientific consensus" is dangerous. It flies in the face
of the history of many wrong guesses. It conjures up the image
of scientific snobbery, and an oligarchial system where people
who don't go along with the "consensus" are marginalized, while
the 95% or more biologists who aren't specialists and who don't
know enough about the issues to say anything intelligent are counted by people like you, Harshman, Simpson and even Ruben as part of the
"consensus".

> not what people prefer,

That's the ideal. The reality includes such things as Padian's
benighted idea that pterosaurs were all bipeds. Reading what Carroll
wrote about it, one would get the impression that this was also
part of the "consensus". Yet one look at those tiny pelvises, and
the angles that the femurs' heads made with them in some species, should have
made it clear how few expertly informed people went into this "consensus".

> and the evidence indicates cladistics shows evolutionary relationships
> more accurately than Linnaean taxonomy does.

There you go again with that artificial use of the word "relationships"
that is so counter to Romer's use of it in Figure 1.

> For example, you proposed
> that under Linnaean taxonomy *Steropodon* and other monotremes would be
> placed inside their own suborder of Monotremata, even though
> *Steropodon* is more closely related to platypuses than to echidnas,

Yeah, and Eohippus is "more closely related" to Equus than it is
to Hyracotherium. Gimme a break.


I'm giving myself a break by snipping the rest of your paragraph,
which ended in a shower of insults.

> >
> >>> And you call yourselves "objective" and "scientific" while denying
> >>> those terms to traditional systematists!
> >>
> >> Yes. I don't understand what argument you are making that cladistic
> >> classification isn't objective or scientific, or perhaps that
> >> traditional classification is either.
> >>
> >> I exhort you to greater effort to make your arguments clear.
> >
> > I think this means: "I exhort you to start making statements that
> > don't rub me the wrong way."
>
> So you willingly refuse to *not* be a dick? Not surprised.

You don't know even 1% of what has gone on between me and Harshman
and his ally Simpson on the "clarity" that Harshman is "exhorting" me to.

Since Simpson has effectively repudiated the agreement we made
years ago, I am willing to tell you all about his shamelessly insincere
use of demands for "clarity," but I would prefer to do it talk.origins, to which our agreement never extended.

> >> Now much of
> >> my current confusion may have to do with your proceeding from false
> >> premises, but I don't think all of it is.
> >
> > I don't think any of it is. And I'd like to see even one example
> > of what you might think to be a false premise behind ANYTHING
> > I've said, whether conducive to confusion in your mind, or not.
>
> Look up the PhyloCode, nitwit, and see what he means by "false premises".

Sorry, I don't accept this attempt by you to read Harshman's mind.

> >
> >
> > Peter Nyikos
> > Professor, Dept. of Mathematics -- standard disclaimer--
> > University of South Carolina
> > http://people.math.sc.edu/nyikos/
> >
> > PS I still haven't replied to the post of yours that I've been
> > hoping to reply to for two days, and it may even have to wait
> > until tomorrow, but at least this one is more than a whole
> > day before the (work) week is out.
> >
>
> Translation: "I'll get to it when I feel like it, even if it's two
> months from now."

You are back to your Thrinaxodon persona here.


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

[John Harshman]

On 8/17/18 5:59 PM, Peter Nyikos wrote:
> Finally, I get a halfway sincere and sane, and almost wholly on-topic,
> reply from Oxyaena!
>
> This will help me to decide just how to handle the request
> John made to both of us in a reply to Oxyaena (mild surprise: not
> to me).

Consider that request made right here, right now. Will that help?

I for one would dearly like to know what you're talking about.

You must understand that the horizontal division also separates closely
related taxa by your definition of "related". Any classification that
splits the tree at any point must divide close relatives. It's a
physical impossibility to do otherwise. Thus the horizontal
classification doesn't have the advantage you suppose.

> That's why I want to get to the bottom of what happened during
> the "cladist wars". I find it very hard to believe that none
> of the traditional systematists didn't press the issue of
> Romer's usage, and adopt it for their own.

The usage of "related" is not really a big issue. And I will point out
again that Romer used it in two contradictory ways on the very page you
reference.

> And in what sense was that particular "cladist war" (or set
> of cladist wars) won by the cladists. Was it put to a democratic
> or oligarchial vote, for example? Under "oligarchial" I include
> basing it on the vote of people registered for and present at a national
> conference.

I think you are taking "cladist wars" too literally. The battles
happened in journals and meetings, but they were won by argument and
persuasion (and of course, eventual retirement and death).

> Many of the most important decisions of the American Mathematical
> Society are oligarcial in this respect.

Evolutionary biology has no such decisions. Anyone is free to do as he
or she pleases and there is no official position, no votes on such
matters. Of course the opinions of editors and reviewers count for
something.

>> Unlike extant organisms, most fossils lack DNA, and therefore the
>> only means left for us to classify them is morphology, and we all know
>> how inaccurate morphologically based phylogenies can get.
>
> That's why I chose the illustrative example I did. The point is,
> how do you split the tree up into groups, once it is decided on?
>
>
>>>>>>> Don't worry, I'll start supporting Yes answers before the week is out,
>>>>>>
>>>>>> Excellent.
>>>
>>> Do you also think it is excellent for you to make unsupported
>>> provocative statements in counterfeit support of your "no"s?
>
>> Your usage of the term "counterfeit" implies that Harshman is being
>> dishonest,
>
> No, he may just be innocently passing on counterfeit "support."
> It was only recently that I learned that the pejorative "unnatural"
> for paraphyletic taxa was not original with him, but had been used
> long ago by C. Patterson.

Wherever could you have gotten the notion that I made up the term? It
isn't original with Patterson either. The search for a natural rather
than artificial classification goes back before Linnaeus. It's our
understanding of what "natural" means that has changed.

> Is the term "disease" something you were uncritically repeating from
> a "research" article like the one by C. Patterson?

I don't even think you've read Patterson directly, just some quote in
Carroll. True?

>> when he is in fact not, and I suggest you refrain from
>> insults when they clearly aren't necessary.
>
> ...glass houses...stones. Look at your parting insult at the end.
>
> I wasn't insulting him, I was characterizing the use of a bald
> assertion to support another bald assertion of "no" to one
> or more of the four questions on the OP.

I would consider it an insult to accuse me of counterfeiting. Your
explanation that you didn't mean it is somewhat less insulting, but
still insulting, as it accuses me of ignorance rather than dishonesty.
Neither is correct.

>>>>>>> John had nothing to say about Hennig's convention, and I suppose you
>>>>>>> don't either.
>>>>>>
>>>>>> Hennig's convention is irrelevant to cladistic classification,
>>>>>> paraphyletic groups, etc.
>>>>>
>>>>> What do you mean? As Carroll points out on p. 13, the result of
>>>>> this convention is that almost exactly half of all species that
>>>>> ever existed were paraphyletic.
>>>>>
>>>>> Another offshoot of this convention is to use the term "hypothetical"
>>>>> for all of them, as though that made them somehow outside the field
>>>>> of science, and safely "out of sight [except for all those pesky
>>>>> nodes], out of mind".
>>>>
>>>> I am unable to interpret that statement.
>
> Are YOU able to interpret it? If not, what is it about it that
> you don't understand?

Why not try to explain what you meant?

[snip the rest, mostly mutual personal attacks between you and Oxyaena]

[Peter Nyikos]

On Monday, August 13, 2018 at 9:57:10 AM UTC-4, John Harshman wrote:
> On 8/13/18 4:44 AM, Peter Nyikos wrote:
> > On Thursday, August 9, 2018 at 5:32:08 PM UTC-4, John Harshman wrote:
> >> On 8/9/18 1:26 PM, Peter Nyikos wrote:
> >
> >>> I explained the concept [of cladophilia] yesterday
> >>> to Oxyaena:
> >>>
> >>> It implies a love of phylogenetic trees, to the
> >>> exclusion of evolutionary trees. The former put all organisms,
> >>> extinct or extant, at the tips of their twigs. The latter put
> >>> as many organisms at nodes as the evidence warrants, showing
> >>> e.g. Merychippus to be ancestral to Equus.
> >>>
> >>> Cladophiles want to banish evolutionary trees from science.
> >>> That is not an insult, that is something all of you are PROUD
> >>> of, because, as you put it, phylogenetic trees show "relationships"
> >>> better than evolutionary trees do.
> >>
> >> I will note that "evolutionary tree" is a bit of propagandistic claiming
> >> of the high ground,
> >
> > Au contraire, it is an effort to claim back SOME ground from the
> > way cladophiles co-opted the words "phylogenetic" and "relationship"
> > to refer to concepts that were once used to refer to direct
> > ancestor-descendant relationships and degree of proximity in morphology
> > [with every effort to distinguish between homology and convergence]
> > IN ADDITION TO the things that they now denote.
>
> Tomato, tomahto.

Is this all the term "claiming of the high ground" means to you?
A matter of personal preference such as the pronunciation of "tomato"?

Is that the way the cladophiles thought of people who used terms
like "disease" for support of paraphyletic taxa, as simply having
different tastes than themselves, and never letting out the slightest
criticism of such language?


> > It is the same way with "monophyly". Because systematists once were
> > perfectly accepting of what Hennig coined the word "paraphyletic" for,
> > they applied "monophyletic" indiscriminately to both kinds of groups.
> >
> > It was to fight this co-optation of "monophyletic" that Ashlock
> > coined the word "holophyletic". These last two days, for the
> > first time, I read what Carroll wrote in his huge _Vertebrate Paleontology
> > and Evolution_ (1988) on pp. 5-6 and 11-13 and was amazed, on the one
> > hand, to see how he meekly went along with the cladophile-friendly version
> > of the term "relationship" and, on the other hand, how critical he was
> > of the cladophile ban on paraphyletic groups and how persistently
> > he used "holophyletic" in an effort to preserve the original meaning
> > of "monophyletic."
> >
> > It's been claimed that Carroll has gone over to the side of the
> > cladists, but was this "going over" anything more than abandoning
> > "holphyletic" in the realization that he was just beating his head
> > against stone walls?
>
> You would have to read his subsequent book, which I have not.

Or you could talk to all those systematists with whom you usually talk to
at conferences. That would be a lot easier.


<snip of things to be addressed next week>


> > Several times, I have made the analogy that one could also have
> > a "cladogram" of mountains, using characters involving geological
> > concepts. And one could easily apply the word "evolution" to what
> > is now called "orogeny".
>
> You have made that claim, but you have never even tried to back it up.

I gave all the necessary backing: any time one has a rank 1 classification
(if two groups overlap, one is a subset of the other) and there is
an algorithm for producing a tree from them just like a phylogenetic
tree: every individual thing at the tips of branches, nothing at the
nodes.

You yourself gave a ridiculous use of this algorithm to produce
a "phylogenetic tree" of Linnean taxa; the difference is that
the line segments connecting one node to the next reflects a
set-subset relationship rather than an ancestral one.


> You could not have a cladogram of mountains

That's why I brought in characters, so you couldn't correctly
make such a claim. Your claim IS valid for the ridiculous use
I mentioned, since many cladograms do go into the use of characters
and all of them are made with the help of characters.


> as anything more than an
> artificial construct that reflects no underlying reality.

There is an underlying reality reflected, just one that does not depict
ancestor-descendant relationships. Exactly as in phylogenetic trees.


> In phylogenetics, on the other hand, common descent is that underlying reality.

But NOT explicit or even implicit in the phylogenetic trees, in which
is forbidden the depiction of evolution as it actually happened -- or
even a hint of how it happened. And that's been my point all along.


Remainder deleted, to be replied to next week. Duty calls.


Peter Nyikos
Professor of Maths -- standard disclaimer--

[John Harshman]

No. I mean that the difference between "claiming of the high ground" and
"claiming back SOME ground from" etc. is so slight that "tomato,
tomahto" is a good description.

> Is that the way the cladophiles thought of people who used terms
> like "disease" for support of paraphyletic taxa, as simply having
> different tastes than themselves, and never letting out the slightest
> criticism of such language?

Who uses terms like "disease"?

>>> It is the same way with "monophyly". Because systematists once were
>>> perfectly accepting of what Hennig coined the word "paraphyletic" for,
>>> they applied "monophyletic" indiscriminately to both kinds of groups.
>>>
>>> It was to fight this co-optation of "monophyletic" that Ashlock
>>> coined the word "holophyletic". These last two days, for the
>>> first time, I read what Carroll wrote in his huge _Vertebrate Paleontology
>>> and Evolution_ (1988) on pp. 5-6 and 11-13 and was amazed, on the one
>>> hand, to see how he meekly went along with the cladophile-friendly version
>>> of the term "relationship" and, on the other hand, how critical he was
>>> of the cladophile ban on paraphyletic groups and how persistently
>>> he used "holophyletic" in an effort to preserve the original meaning
>>> of "monophyletic."
>>>
>>> It's been claimed that Carroll has gone over to the side of the
>>> cladists, but was this "going over" anything more than abandoning
>>> "holphyletic" in the realization that he was just beating his head
>>> against stone walls?
>>
>> You would have to read his subsequent book, which I have not.
>
> Or you could talk to all those systematists with whom you usually talk to
> at conferences. That would be a lot easier.

How would that help me? Are you suggesting I take a poll? I don't think
many of the people I know also know Carroll. Or read his book. Anyway,
what does it matter whether Carroll recanted on his deathbed? Why are we
even talking about this?

>>> Several times, I have made the analogy that one could also have
>>> a "cladogram" of mountains, using characters involving geological
>>> concepts. And one could easily apply the word "evolution" to what
>>> is now called "orogeny".
>>
>> You have made that claim, but you have never even tried to back it up.
>
> I gave all the necessary backing: any time one has a rank 1 classification
> (if two groups overlap, one is a subset of the other) and there is
> an algorithm for producing a tree from them just like a phylogenetic
> tree: every individual thing at the tips of branches, nothing at the
> nodes.

That wasn't even a sentence. What happens anytime? I don't think you
have a clear idea how phylogenetic trees are produced or even, perhaps,
what they signify.

> You yourself gave a ridiculous use of this algorithm to produce
> a "phylogenetic tree" of Linnean taxa; the difference is that
> the line segments connecting one node to the next reflects a
> set-subset relationship rather than an ancestral one.

What algorithm are you referring to, and what ridiculous use was that? I
disremember.

>> You could not have a cladogram of mountains
>
> That's why I brought in characters, so you couldn't correctly
> make such a claim. Your claim IS valid for the ridiculous use
> I mentioned, since many cladograms do go into the use of characters
> and all of them are made with the help of characters.

I don't know what ridiculous use you were mentioning. I don't know what
you think you're saying here. I doubt you, personally, could produce a
cladogram of mountains, as your attempted partial example of how you
might do it made no sense.

Remind me what point you are trying to make by claiming that there could
be a cladogram of mountains.

>> as anything more than an
>> artificial construct that reflects no underlying reality.
>
> There is an underlying reality reflected, just one that does not depict
> ancestor-descendant relationships. Exactly as in phylogenetic trees.

I don't think that's true at all. We could get into an argument about
how one would go about showing that phylogenetic trees reflect reality,
and how such a process would not show that your tree of mountains did,
but that would be a long, difficult, off-topic conversation.

>> In phylogenetics, on the other hand, common descent is that underlying reality.
>
> But NOT explicit or even implicit in the phylogenetic trees, in which
> is forbidden the depiction of evolution as it actually happened -- or
> even a hint of how it happened. And that's been my point all along.

If that's your point, it's just wrong. You don't know how to interpret a
phylogenetic tree. Nor do you know what evolution as it actually
happened is, if by that you mean ancestor-descendant sequences.
Fortunately, we don't need such sequences to know everything we can
actually know about evolution. But phylogenetic trees are quite useful
for that purpose, if you have any idea of how to use them.

[Oxyaena]

On 8/17/2018 8:59 PM, Peter Nyikos wrote:
[snip repetitive bullshit]

>
>>>>>>> Don't worry, I'll start supporting Yes answers before the week is out,
>>>>>>
>>>>>> Excellent.
>>>
>>> Do you also think it is excellent for you to make unsupported
>>> provocative statements in counterfeit support of your "no"s?
>
>> Your usage of the term "counterfeit" implies that Harshman is being
>> dishonest,
>
> No, he may just be innocently passing on counterfeit "support."
> It was only recently that I learned that the pejorative "unnatural"
> for paraphyletic taxa was not original with him, but had been used
> long ago by C. Patterson.
>
> Is the term "disease" something you were uncritically repeating from
> a "research" article like the one by C. Patterson?

It was sarcasm, asshole. I've told you this before.

>
>
>> when he is in fact not, and I suggest you refrain from
>> insults when they clearly aren't necessary.
>
> ...glass houses...stones. Look at your parting insult at the end.
>
> I wasn't insulting him, I was characterizing the use of a bald
> assertion to support another bald assertion of "no" to one
> or more of the four questions on the OP.

Calling it "counterfeit" is still insulting him, no matter what bullshit
rationalizations you come up with to justify the insult.

I did, but nothing aside from this bald assertion of yours indicates as
much, given your rabid hatred towards cladistics otherwise. If you have
to clarify you don't prefer Linnaean taxonomy over cladistics, perhaps
you should word better your posts on this subject.

>
>
>> *Why* do you think Linnaean taxonomy is preferable to
>> cladistics? Are you even *capable* of answering those questions?
>
> This is one reason I wrote "halfway" before "sincere and sane." AT BEST,
> you are baselessly guessing false "facts" about me. At worst...
> well, if you are halfway sane, you can correctly guess what
> those ellipses are shorthand for.

Yet another reason you are still a dishonest prick, because I'm
perfectly sane. You're insulting me by putting "half-way". Grow up.

>
>
>>
>>>
>>>> which can be turned into a description of that unknown
>>>> ancestor. Of course that description is an estimate, as everything in
>>>> science.
>>>
>>> Including "ancestor candidate," but you are against accepting
>>> that in science, aren't you?
>
> Same question to you, Oxyaena.

I think the issue is mere semantics, classifying something as a
potential "ancestor candidate" is at least somewhat more justifiable
than pointing to something as the definitive ancestor. One must take
into account the notorious scarcity of the fossil record, most organisms
don't get fossilized, so anything we find in the fossil record is more
likely to be a close cousin to the actual ancestor of anything alive
today than its actual ancestor, and this gets truer the farther back in
the fossil record one goes.

Here you go with your mind-reading tactics, I didn't respond to it
because I had nothing to add to it. Unlike you, I don't pretend to read
minds. It looks as if the discussion was already settled. I fully agree
with you here. I've said many times before that I`m not on opposing
sides, Peter, I think cladistics should be reformed as well, but I don't
think Linnaean taxonomy is the way to do it.

>
>
>
>>>> but since nobody is defending that silly
>>>> convention there seems no point.
>>>
>>> Where did you even hint, before here, that this particular convention by
>>> Hennig was silly? And is your opinion your own, or is it the "consensus"
>>> of systematists?
>>
>> How many times do I have to explain to you that the scientific consensus
>> is based off of the evidence available at hand,
>

[snip irrelevant drivel]

>
>> not what people prefer,
>
> That's the ideal. The reality includes such things as Padian's
> benighted idea that pterosaurs were all bipeds. Reading what Carroll
> wrote about it, one would get the impression that this was also
> part of the "consensus". Yet one look at those tiny pelvises, and
> the angles that the femurs' heads made with them in some species, should have
> made it clear how few expertly informed people went into this "consensus".
>

I never realized that there was *any* consensus about pterosaurs being
bipeds, if anything they were crawlers, using their wings as forelimbs
on the ground, since they were quadrupedal on the ground.

>
>> and the evidence indicates cladistics shows evolutionary relationships
>> more accurately than Linnaean taxonomy does.
>
> There you go again with that artificial use of the word "relationships"
> that is so counter to Romer's use of it in Figure 1.

Why are you against the term "relationship". You wouldn't say that
chimps and humans aren't "closely related" because of some utterly
pointless pet peeve against cladistics.

>
>
>
>> For example, you proposed
>> that under Linnaean taxonomy *Steropodon* and other monotremes would be
>> placed inside their own suborder of Monotremata, even though
>> *Steropodon* is more closely related to platypuses than to echidnas,
>
> Yeah, and Eohippus is "more closely related" to Equus than it is
> to Hyracotherium. Gimme a break.

*Hyracotherium* is in another family entirely. You're implying that
*Eohippus* and *Hyracotherium* should be placed in their own,
polyphyletic, taxon rather than *Hyracotherium* and *Eohippus* being
placed inside their own respective clades. It's not even paraphyletic,
since *Eohippus* is an equiid while *Hyracotherium* is a palaeotheriid,
in order to "make" it paraphyletic one would need to reclassify the
whole of early Perissodactyla.

>
>
> I'm giving myself a break by snipping the rest of your paragraph,
> which ended in a shower of insults.

You mean this:

"...and I retorted that would give the false impression that Mesozoic

monotremes were a single monophyletic clade, and their descendants an
entirely different clade, arbitrarily distinguished from each other when
there was no such distinguishing basis in actuality. You usually ignore
when I bring this up because it inconveniences you, and I suspect you
will do so here, or dishonestly snip it, whichever one suits you best."

The fact that there a few insults in there provides you plenty of excuse
to ignore the majority of what I wrote, at least *try* to respond to it
instead of conveniently, and dishonestly, pretending it was nothing but
a "shower of insults".

>
>
[snip personal attacks and baseless accusations by Nyikos]
>

--
"There is only one good, knowledge, and one evil, ignorance." -
Socrates, as recorded by Diogenes Laertius

[Peter Nyikos]

On Friday, August 17, 2018 at 9:33:35 PM UTC-4, John Harshman wrote:
> On 8/17/18 5:59 PM, Peter Nyikos wrote:
> > Finally, I get a halfway sincere and sane, and almost wholly on-topic,
> > reply from Oxyaena!
> >
> > This will help me to decide just how to handle the request
> > John made to both of us in a reply to Oxyaena (mild surprise: not
> > to me).

The mild surprise was occasioned by the fact that when Erik and I went
at each other, your first reply was to me, and only the second such reply
went to Erik after a wholly new phase of our being at loggerheads
with each other.

> Consider that request made right here, right now. Will that help?

Gratuitous redundancy is never helpful. What would have been helpful
would have been advice on how to go about disengaging myself, and
what to do if Oxyaena doesn't follow suit. See my PS at the end.

Your ignorance of this debate makes me wonder just how fragmentary
your knowledge of the "cladist wars" actually is.

At a now-famous meeting of vertebrate zoologists
[*sic*: not "paleontologists"]
in Reading, England, in 1978, the zoological conundrum
about the lungfish, the salmon, and the cow caused a mild
sensation. In retrospect it should not have caused more
than a blink of the eye. The most obvious answer is,
of course, that the two fishes *appear* to be more closely
related than either is to a cow. Both are fishes, after all.
But ... blink the eye, and it is evident that the lungfish
and the cow are more closely *related* (although physically
less similar) because they both belong on the closer line
of descent.
-- Keith S. Thomson, _Living Fossil: the Story of the
Coelacanth_. W.W. Norton & co., 1991. pp. 204-205

Note how this distinguished former dean and CEO of "the Academy of
Natural Sciences in Philadelphia" at the time of writing takes it
for granted, in a book pitched at a general audience, that his
readers will go along with a concept of "more closely related"
that is so completely at variance with the usual layman's idea
of close relationship.

The trio of {{cow, *Elginerpeton*} , *Tiktaalik*} shows where
that concept logically takes one. Did you look at the webpage
I linked up there? The two latter would fit rather comfortably
in the same Linnean order and probably family, and would thus
be far more closely related than the first two, according to
Fig. 1 in Romer's text.

More about Fig. 1 below.

As I was saying earlier:

> >>>>> Worse yet, they either did not know how Romer 1945 used the term
> >>>>> "closely related " in a completely different way than the
> >>>>> way I've seen it used in every account I've seen so far,
> >>>>> or else we have another example of "history is written by the victors."
> >>>>>
> >>>>> That reminds me: did you see whether the 1966 edition has something
> >>>>> fitting the description I gave you of Fig. 1 of the 1945 edition
> >>>>> in a post of yesterday? You haven't replied to that post yet.
> >>>>
> >>>> Yes, I saw it, and I suspect the text didn't change either. To the
> >>>> extent Romer's text contains an argument for paraphyly, that argument is
> >>>> seriously flawed.
> >>>
> >>> I see you are tenaciously clinging to your lack of support for
> >>> "no, no, no, and no," and even for provocative comments like
> >>> the one you've just made, which would at least initiate a support
> >>> for one or more "no"s.
> >>>
> >>> On the other hand, I begin to support a Yes answer to 2. later
> >>> in this post.
> >>>
> >>>
> >>>> Ironically, the inclusion of fossils makes it more
> >>>> flawed than if he had considered only extant species.
> >>>
> >>> I think the opposite is true, and I'll explain in detail when
> >>> I have more time to spare. Meanwhile, your tenacious clinging
> >>> to your policy is exacerbated by the leading word "Ironically."
> >>>
> >>
> >> Why?

Because you are being less clear in the last two things you
wrote in that earlier reply, than I have ever been about anything
in the 7+ years we've argued in talk.origins and s.b.p. -- your
"exhortations" to me to be "more clear" notwithstanding.

And you seem perfectly content to stay that way.

Tell me about something that I haven't understood since the age of 11.

> Any classification that
> splits the tree at any point must divide close relatives. It's a
> physical impossibility to do otherwise. Thus the horizontal
> classification doesn't have the advantage you suppose.

I never supposed any such thing. What's more, this is another
huge lapse of memory about the compromise I talked about
explicitly in my reply to your OP.

You keep deleting my comments about evidence for Alzheimer's,
including the one that was preceded by praise for you
becoming proactive at last [in stunning contrast to your
conspicuous lack of clarity up there, reinforced by your "Why?"].

You even took umbrage at one of my reminders. This suggests
that you know that your memory is not what it used to be,
yet are in denial about finding out the extent of the change.

> > That's why I want to get to the bottom of what happened during
> > the "cladist wars". I find it very hard to believe that none
> > of the traditional systematists didn't press the issue of
> > Romer's usage, and adopt it for their own.
>
> The usage of "related" is not really a big issue.

It's a shame that the traditional systematists didn't make it one,
unless they did, and history is being rewritten by the victors.

> And I will point out
> again that Romer used it in two contradictory ways on the very page you
> reference.

I have never seen, before, anyone except Marxists use the word
"contradiction" and its derivatives in the way you are using it here.

[Not that I have anything against Marxists as a whole. There have
been some very fine people among them, including IIRC Stephen Jay Gould.]

You mean "two contrasting ways" or actually, "two ways that are
different yet totally compatible with each other."

I take it you are referring to the following in Fig. 1.

[The vertical classification] makes clear the relation
[*sic*: not "close relation"] of early ancestors (A' B')
to their descendants but separates them sharply from C,
the common ancestor, and other side branches, such as D,

to which they are closely related.

Note where the term "closely related" is used -- exactly the way
it is used in human genealogies.

If you can't see the truth of "two ways that are
different yet totally compatible with each other," then
here is evidence that Alzheimer's may be affecting more
than just your memory, and I exhort you to re-read the post
where I praised you for your efforts at becoming more proactive.


Remainder deleted, to be replied to later.


Peter Nyikos
Professor, Department of Mathematics -- standard disclaimer--

University of South Carolina
http://people.math.sc.edu

PS. In lieu of any suggestions by you as to how to word it,
I will announce my new policy on Oxyaena later today.

[Oxyaena]

On 8/20/2018 11:14 AM, Peter Nyikos wrote:
> On Friday, August 17, 2018 at 9:33:35 PM UTC-4, John Harshman wrote:
>> On 8/17/18 5:59 PM, Peter Nyikos wrote:
>>> Finally, I get a halfway sincere and sane, and almost wholly on-topic,
>>> reply from Oxyaena!
>>>
>>> This will help me to decide just how to handle the request
>>> John made to both of us in a reply to Oxyaena (mild surprise: not
>>> to me).
>
> The mild surprise was occasioned by the fact that when Erik and I went
> at each other, your first reply was to me, and only the second such reply
> went to Erik after a wholly new phase of our being at loggerheads
> with each other.
>
>> Consider that request made right here, right now. Will that help?
>
> Gratuitous redundancy is never helpful. What would have been helpful
> would have been advice on how to go about disengaging myself, and
> what to do if Oxyaena doesn't follow suit. See my PS at the end.
>

I will follow suit, because this is honestly good news, it means you're
considering ending your bullshit trolling and will get back to not
flaming me and actually posting on-topic material to sbp. I'm still
skeptical about whether you'll keep your word on this matter.

And that's where Linnaean taxonomy fails. *Elginerpeton* is a
sarcopterygian, a salmon is an actinopterygian, the two clades diverged
long before lungfish and *Elginopterpeton* came about, and the genome of
a lungfish therefore more closely resembles a cow's genome than a
salmon's genome. This doesn't even have to do with the everyday meaning
of the term "closely related", lungfish are more closely related to cows
than they are to salmon, irregardless of what definition you use for the
term "closely related". Linnaean taxonomy falls apart when it comes to
accurately showing phylogenetic relationships, while cladistics does a
better job at it.

Cue whining about how "cladophiles" co-opted the term "closely related".

These are all insults, or personal matters that Harshman doesn't want to
talk about, you bringing it up again even after he asked you to stop
shows that you're categorically incapable of recognizing your own faults.

>
>>> That's why I want to get to the bottom of what happened during
>>> the "cladist wars". I find it very hard to believe that none
>>> of the traditional systematists didn't press the issue of
>>> Romer's usage, and adopt it for their own.
>>
>> The usage of "related" is not really a big issue.
>
> It's a shame that the traditional systematists didn't make it one,
> unless they did, and history is being rewritten by the victors.
>
>
>> And I will point out
>> again that Romer used it in two contradictory ways on the very page you
>> reference.
>
> I have never seen, before, anyone except Marxists use the word
> "contradiction" and its derivatives in the way you are using it here.
>
> [Not that I have anything against Marxists as a whole. There have
> been some very fine people among them, including IIRC Stephen Jay Gould.]
>

"I`m not prejudiced, but..."

>
> Peter Nyikos
> Professor, Department of Mathematics -- standard disclaimer--
> University of South Carolina
> http://people.math.sc.edu
>
> PS. In lieu of any suggestions by you as to how to word it,
> I will announce my new policy on Oxyaena later today.
>

I'll be glad to hear it, so I can finally be done with the burden of
having to address the libels you've written about me. Let's see if you
can hold up your promise.

--
"Right action is always better than right knowledge, but in order to do
what is right, we must *know* what is right." - Charlemagne

[Peter Nyikos]

On Thursday, August 16, 2018 at 6:00:29 PM UTC-4, Oxyaena wrote:
> On 8/16/2018 3:20 PM, Peter Nyikos wrote:
> > On Thursday, August 16, 2018 at 1:57:51 PM UTC-4, Oxyaena wrote:
> >> On 8/16/2018 7:54 AM, Peter Nyikos wrote:
> >> [snip personal attacks and baseless accusations by Nyikos]
> >
> > You are in deep denial over how thoroughly those accusations
> > were documented and reasoned.

The deep denial continues:

> Bullshit. I need documentation.

Done already, several times, both here and in talk.origins.
Anyone going back over this thread can see the documentation,
including a link to the following:


https://groups.google.com/d/msg/talk.origins/Xub9hqEyM0A/l7gpBG1zCAAJ
Subject: Re: The evolution of the bacterial flagellum: For Peter
Date: Fri, 27 Jul 2018 10:08:39 -0700 (PDT)
Message-ID: <8174902f-492c-4d99...@googlegroups.com>

This was in direct reply to your post where you libeled me,
as recounted below for the nth time on s.b.p. ( n at least 3).

> Put up or shut up, neither of which
> you're seemingly capable of doing.

I'm sure you know by now that the following was not a
slander at all:

you *also* showed your ignorance about when life
could reasonably be expected to arise and evolve in our universe.

and so you slandered me with the following "description" of this
simple two liner:

In short, another demonstration of your
dishonesty, blatant distorting of the facts, and outright slander.
I could sue you for libel, Peter, but unlike you I`m a decent
person so I won't.


In fact, you know by now that the following claim by you,
described by my simple two liner, was indicative of ignorance by you:

Considering that the universe is only 13.8 billion years old, and the
universe only settled down enough for life to develop some 4.5 Ga, ala
when our Solar System formed,

Note, your claim isn't about life on earth, it is about the universe
as a whole. The last time I showed you these words, you ran away
with a completely unquantified claim that the "early" universe was
a wild place. But you knew, from what I documented in the same post
where you made the evasion, that it is scientific consensus that
"early" in this sense ended WELL before 6.5 billion years ago.

Note, 6.5, not 4.5 as you claimed.

Why do I say 6.5 billion? because of what I also documented
in the talk.origins post I linked above:

By the way, the planetary system within 100 light years of us
that SETI considered the best target for a long time
is Delta Pavonis, a G star like our sun. It is estimated to be
over 6.5 billion years old, yet has a higher percentage of
heavy elements than our sun.

https://en.wikipedia.org/wiki/Delta_Pavonis

The only reply anyone has EVER made to the post I linked up there
was you, digging yourself in deeper with a two-line reply:

[snip mindless bullshit]

Fixed it for you, Petey.

And the whole post to which I am replying here and now consists
of you digging yourself in, in the same use of Truth by Blatant
Assertion.

> > Moreover, you are "forgetting" that you also
> > snipped some meaty paleontology by myself. In which I caught
> > you in an embarrassing error, to boot.
>
> What paleontology, and what "error"? You're pulling things out of thin
> air. Can you see things others can't?

You saw it yourself, and made the same snarky kind of reply
to the post where it occurred:

________________________ excerpt ___________________

> I should also add that he left out *why* I disagree with him on this
> issue, namely that Linnaean taxonomy doesn't do a good job of
> representing evolutionary relationships, cladistics does a far better
> job at it, since Linnaean taxonomy would place chimps and other apes in
> Pongo,

Pongo is the scientific name for the orangutan.

You mean Pongidae. But even that would probably have been changed
by now, were Linnean classification not so universally despised.
After all, it came to reject "Pithecanthropus" and put it in
*Homo erectus*.

==================== end of excerpt ========================

There is no need to give an url, etc. because it is only three
posts DIRECTLY upstream from the post of yours to which I am
replying now.


I've snipped the remainder, since your contribution was all Truth
by Blatant Assertion. It was exactly the kind of bizarre blustering
that is so evident in the two examples above.

Evidently that kind of blustering was already prevalent
when it inspired Monty Python to create the Black Knight character
in "Monty Python and the Holy Grail."

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina

http://www.math.sc.edu/~nyikos/

[Peter Nyikos]

That isn't quite true, John. You saw an integral part of the
"mutual harangue" and replied to it:

_____________________excerpt ____________________________________
>> "fuckwad" is not an insult in your vocabulary???

>>
>>> but apparently you're all too willing to act like the immature
>>> sociopath you are rather than leave sbp out of the nonsense you conduct
>>> in talk.origins.
>>

>> I see you did make ample loopholes in your "agreement" to
>> be civil, or whatever, in s.b.p. It sure isn't anything like the
>> agreement Richard Norman, John Harshman, Erik Simpson and I
>> made over 4 years ago to leave aside personal animosities in
>> talk.origins and to treat s.b.p. as a sort of "embassy," with
>> us behaving like good ambassadors.
>
>
> I meant the post you originally responded to, jackass. Are you not able
> to read?

It's not necessary to be insulting. You can achieve your points without
it. Added bonus: you can feel smug for maintaining good manners.

====================== end of excerpt from
https://groups.google.com/d/msg/sci.bio.paleontology/RNINuDOndSM/QTxDZmfwBQAJ
Date: Wed, 1 Aug 2018 14:53:29 -0700
Message-ID: <IPednZacT5ZEtv_G...@giganews.com>

Subject: Re: Pterosaur dietary hypotheses

I don't think smugness is a trait to be encouraged in anyone,
let alone someone as volatile as Oxyaena. Do you disagree?

Don't get me wrong: I am not accusing you of contributing
to the intensity of Oxyaena's rampage. You obviously had no
idea of what the future had in store.


Anyway, I will announce a kind of moratorium later today.
I will need to give it plenty of thought, given the way
Oxyaena exploits loopholes in things like her original
agreement to "let bygones be bygones".


Peter Nyikos

[Oxyaena]

On 8/20/2018 2:02 PM, Peter Nyikos wrote:
[snip libel by Nyikos]

Harshman asked me to stop feeding your trolling habits, which I've been
doing, so I`m not going to dignify your gibberish with a response.
Peter, I kindly ask you stop trying to flame me and libel me, even when
I've pointed out numerous times to stop doing so and have documented how
you were doing so, and I also ask you to stop snipping half of my posts
whenever you respond to me.

This is the last post I will be making on this thread, as far as it
pertains to your flaming of me. I will only reply to on-topic posts of
yours, since responding to your trolling only clutters up the thread.

Your response to this post will give me the answer I need as to whether
I should continue to respond to you at all or not.

[Oxyaena]

You use quotation marks as if you're innocent of any wrongdoing, you
hypocritical liar.

>
> _____________________excerpt ____________________________________
>>> "fuckwad" is not an insult in your vocabulary???
>>>
>>>> but apparently you're all too willing to act like the immature
>>>> sociopath you are rather than leave sbp out of the nonsense you conduct
>>>> in talk.origins.
>>>
>>> I see you did make ample loopholes in your "agreement" to
>>> be civil, or whatever, in s.b.p. It sure isn't anything like the
>>> agreement Richard Norman, John Harshman, Erik Simpson and I
>>> made over 4 years ago to leave aside personal animosities in
>>> talk.origins and to treat s.b.p. as a sort of "embassy," with
>>> us behaving like good ambassadors.
>>
>>
>> I meant the post you originally responded to, jackass. Are you not able
>> to read?
>
> It's not necessary to be insulting. You can achieve your points without
> it. Added bonus: you can feel smug for maintaining good manners.
>
> ====================== end of excerpt from
> https://groups.google.com/d/msg/sci.bio.paleontology/RNINuDOndSM/QTxDZmfwBQAJ
> Date: Wed, 1 Aug 2018 14:53:29 -0700
> Message-ID: <IPednZacT5ZEtv_G...@giganews.com>
> Subject: Re: Pterosaur dietary hypotheses
>
>
> I don't think smugness is a trait to be encouraged in anyone,
> let alone someone as volatile as Oxyaena. Do you disagree?
>

So you want to insult me behind my back while pretending to be the
victim? Dull surprise.

> Don't get me wrong: I am not accusing you of contributing
> to the intensity of Oxyaena's rampage. You obviously had no
> idea of what the future had in store.

The amount of smugness, psychological projection, and arrogant
self-righteousness in this paragraph of yours is off the charts, Nyikos.

>
>
> Anyway, I will announce a kind of moratorium later today.

Good, let's see it. So far you've done nothing to indicate that you're
ever going to stop flaming me, and the most recent reply to me by you is
the exact opposite of what you're saying to Harshman. In other words,
you're a two-faced liar.

> I will need to give it plenty of thought, given the way
> Oxyaena exploits loopholes in things like her original
> agreement to "let bygones be bygones".

You will definitely need to give it plenty of thought, so you can add in
all those loopholes that you love to use against me and accuse me of
doing. Note that I stopped being civil towards you months after that
agreement, since you kept libeling me anyways behind my back, and I
decided enough is enough. I`m a very patient person, Nyikos, I'd have to
be to deal with the likes of you, but even my patience has worn thin
when it comes to your shenanigans.


>
>
> Peter Nyikos

[Peter Nyikos]

On Monday, August 20, 2018 at 12:23:16 PM UTC-4, Oxyaena wrote:
> On 8/20/2018 11:14 AM, Peter Nyikos wrote:
> > On Friday, August 17, 2018 at 9:33:35 PM UTC-4, John Harshman wrote:
> >> On 8/17/18 5:59 PM, Peter Nyikos wrote:
> >>> Finally, I get a halfway sincere and sane, and almost wholly on-topic,
> >>> reply from Oxyaena!
> >>>
> >>> This will help me to decide just how to handle the request
> >>> John made to both of us in a reply to Oxyaena (mild surprise: not
> >>> to me).
> >
> > The mild surprise was occasioned by the fact that when Erik and I went
> > at each other, your first reply was to me, and only the second such reply
> > went to Erik after a wholly new phase of our being at loggerheads
> > with each other.
> >
> >> Consider that request made right here, right now. Will that help?
> >
> > Gratuitous redundancy is never helpful. What would have been helpful
> > would have been advice on how to go about disengaging myself, and
> > what to do if Oxyaena doesn't follow suit. See my PS at the end.
> >
>
> I will follow suit,

Use of future tense noted. We seem to be on the same page here.

<snip present trolling by you>

Correction: that is where Linnean taxonomy makes a contribution
to systematics that supplements the equally one-sided contribution
of cladistic systematics. The pros and cons of each system are
introduced very well in Romer's Fig. 1.

> *Elginerpeton* is a
> sarcopterygian, a salmon is an actinopterygian,

Even before last week, I criticized the choice of salmon even
among extant organisms, by way of explaining how the
traditional systematists really botched the choice of taxa -- if indeed
it wasn't foisted on them by the cladophiles.

You have some catching up to do here.


[snip harping on salmon, done later on the same page by
Keith S. Thompson anyway]

> Cue whining about how "cladophiles" co-opted the term "closely related".

All these years, have you really missed my repeated skewering of this
use of the word "whining"??

WHINE: an inchoate concept as used on Usenet;
were it made logically consistent and defined
broadly enough to encompass the most influential
uses in talk.origins, it would mean
"anything that can be construed,
in however strained a way, as a complaint,"
and hence would encompass much or all
of each of the following:
the Declaration of Independence, the Communist
Manifesto, Martin Luther King's "I have a
dream" speech, Mark Antony's funeral oration
in Shakespeare's _Julius Caesar_,
John the Baptist's denunciation of
Herod Antipas, and Jesus's "woe to you, scribes
and Pharisees, hypocrites" rant [more at RANT].


Sometimes, when I've posted this in the past, some "peanut gallery"
types drooled all over their keyboards that I am "equating"
myself with the people I've named above. Of course,
as any normal adult can see, what I am doing is
using these familiar examples to illustrate the logical consequences
of the massive intellectual inbreeding to which the word "whine" has
been subjected in highly charged forums like talk.origins.

The latter, if you read the actual posts where I called attention
to these lapses, especially the post where I gave A for effort to John
for being proactive for a change.

> that Harshman doesn't want to
> talk about,

Harshman has told me many times that my wants are of no
interest. I don't even think he adds "to me" when he does this.

Similarly, his wants are of no interest to me. Legitimate concerns
are a different issue altogether.

> you bringing it up again even after he asked you to stop

Document where he did this concerning the above issues, or retract.

> >>> That's why I want to get to the bottom of what happened during
> >>> the "cladist wars". I find it very hard to believe that none
> >>> of the traditional systematists didn't press the issue of
> >>> Romer's usage, and adopt it for their own.
> >>
> >> The usage of "related" is not really a big issue.
> >
> > It's a shame that the traditional systematists didn't make it one,
> > unless they did, and history is being rewritten by the victors.
> >
> >
> >> And I will point out
> >> again that Romer used it in two contradictory ways on the very page you
> >> reference.
> >
> > I have never seen, before, anyone except Marxists use the word
> > "contradiction" and its derivatives in the way you are using it here.
> >
> > [Not that I have anything against Marxists as a whole. There have
> > been some very fine people among them, including IIRC Stephen Jay Gould.]
> >
>
> "I`m not prejudiced, but..."

Typical mindless leftist retort noted.

Besides, the bracketed aside was just to ward off the very
sort of leftist harangue at which you are hinting.

>
> >
> > Peter Nyikos
> > Professor, Department of Mathematics -- standard disclaimer--
> > University of South Carolina
> > http://people.math.sc.edu
> >
> > PS. In lieu of any suggestions by you as to how to word it,
> > I will announce my new policy on Oxyaena later today.
> >
>
> I'll be glad to hear it, so I can finally be done with the burden of
> having to address the libels you've written about me.

That burden is nonexistent, as I documented in a post today
where you libeled me with the charge that I had libeled you.
What I had done instead was to thoroughly document a libel
by you that originated in talk.origins and has been tenaciously adhered to
both there and here in sci.bio.paleontology.

If you go on libeling me after I've announced my policy
later today, don't expect me to correct you.

Will that whet your appetite for further libels? Only time will tell.

> Let's see if you
> can hold up your promise.

That knife cuts both ways.


Peter Nyikos
Professor of Mathematics -- standard disclaimer--
University of South Carolina
http://www.math.sc.edu/~nyikos/

[Peter Nyikos]

Oxyaena goes on libeling me below, copiously, despite minuscule
provocation by me this time around.

In a weak sort of warm-up for my announcement later today,
I only reply in the one place where one might give Oxyaena's
misrepresentation the benefit of the doubt.

I was quoting Harshman, and you don't seem to realize that I
wasn't contesting what I quoted. There WAS a mutual harangue
going on (and still is). The huge difference is that your harangue has
ridden roughshod over admonitions like the following, whereas my harangue
scrupulously respects them:

Woe unto them that call evil good, and good evil; that put
darkness for light, and light for darkness... Isaiah 5:20

The quotation from Charlemagne at the end also speaks to the difference
between moral right and wrong, and you have been heedless of it for
weeks now.


Peter Nyikos

[Peter Nyikos]

On Wednesday, August 15, 2018 at 11:58:01 AM UTC-4, Oxyaena wrote:
> On 8/15/2018 10:20 AM, Peter Nyikos wrote:
> > On Wednesday, August 15, 2018 at 7:27:41 AM UTC-4, Peter Nyikos wrote:
> >> On Tuesday, August 14, 2018 at 1:46:50 PM UTC-4, Oxyaena wrote:
> >>> On 8/14/2018 12:48 PM, Peter Nyikos wrote:
> >>>> On Monday, August 13, 2018 at 1:40:47 PM UTC-4, Oxyaena wrote:
> >>>>> ,
> >>>>>>
> >>>>>> "we" is inappropriate since you have consistently fought
> >>>>>> against the word "cladophile", though not as emotionally
> >>>>>> as Oxyaena.
> >>>>>
> >>>>> You deliberately lie about what I wrote to you as being merely
> >>>>> "emotional".
> >>>>
> >>>> "what I wrote to you" goes back about five years, to where you
> >>>> first decided to target me for abuse under your old moniker
> >>>> "Thrinaxodon." For the first year or so I was just scratching
> >>>> my head, figuratively speaking, to figure out why you were doing
> >>>> this, because you almost never tried to establish a firm connection
> >>>> between anything I had done and the abuse that you showered on me.
> >>>>
> >>>> What you reposted below is cherry-picked out of all the things
> >>>> you've posted in reply to me, back when you were in a
> >>>> "Dr. Oxyaena Jekyll" frame of mind.
> >>>
> >>> You must love portraying the people you hate the most as two-dimensional
> >>> monsters and not as actually being multifaceted people.
> >>
> >>
> >>>> There was no falsehood, let alone lying, involved in my
> >>>> saying that this comment, made in your "Thrinaxodon Hyde"
> >>>> frame of mind, was emotional:

> >>>>
> >>>> I didn't read all the way through, since the cladophobe bullshit
> >>>> infested every corner of my screen I quickly clicked out of it lest I
> >>>> get your disease.
> >>>> https://groups.google.com/d/msg/sci.bio.paleontology/RNINuDOndSM/cy3gGiLiBQAJ
> >>>>

> >>>> This, I think, expresses your true attitude towards Linnean taxonomy,
> >>>> complementing your polite but unscientific comments in response
> >>>> to what I wrote and you are quoting below.
> >>>
> >>> Specify, how exactly is what I wrote "unscientific".
> >>
> >> Your whole argument rests on endless repetition of a claim that
> >> rests on a self-serving, unhistorical, arbitrary and unscientific
> >> use of the term "more closely related."
> >>
> >> But
> >
> > My apologies. I meant to hit "Discard" and hit "Post" instead.
> > I had decided there were more important things to respond to,
> > like Harshman's post of two days ago that I haven't answered yet. Even
> > that will have to wait until later today.
> >
> > Like I told Oxyaena a few minutes ago, I will respond to the
> > rest of her/his post [snipped, below] on my own good time.
> >
>
> Which means "never".

Here is one place where you indirectly issued a challenge
for me to prove you wrong and thus feed the troll -- yourself.

Of course, it pretends that I will be making a radical break
from the harangue that had already taken place between us
for some time.


But be of good cheer: you may wind up having told the truth
for once. All depends on how the moratorium I will announce
today plays out.

Peter Nyikos

[John Harshman]

On 8/20/18 8:14 AM, Peter Nyikos wrote:
> On Friday, August 17, 2018 at 9:33:35 PM UTC-4, John Harshman wrote:
>> On 8/17/18 5:59 PM, Peter Nyikos wrote:
>>> Finally, I get a halfway sincere and sane, and almost wholly on-topic,
>>> reply from Oxyaena!
>>>
>>> This will help me to decide just how to handle the request
>>> John made to both of us in a reply to Oxyaena (mild surprise: not
>>> to me).
>
> The mild surprise was occasioned by the fact that when Erik and I went
> at each other, your first reply was to me, and only the second such reply
> went to Erik after a wholly new phase of our being at loggerheads
> with each other.
>
>> Consider that request made right here, right now. Will that help?
>
> Gratuitous redundancy is never helpful. What would have been helpful
> would have been advice on how to go about disengaging myself, and
> what to do if Oxyaena doesn't follow suit. See my PS at the end.

That too seems simple enough: don't respond to insults or don't respond
to posts containing insults; don't indulge in insults yourself. If
Oxyaena doesn't follow suit, ignore more.

Not helpful.

> At a now-famous meeting of vertebrate zoologists
> [*sic*: not "paleontologists"]
> in Reading, England, in 1978, the zoological conundrum
> about the lungfish, the salmon, and the cow caused a mild
> sensation. In retrospect it should not have caused more
> than a blink of the eye. The most obvious answer is,
> of course, that the two fishes *appear* to be more closely
> related than either is to a cow. Both are fishes, after all.
> But ... blink the eye, and it is evident that the lungfish
> and the cow are more closely *related* (although physically
> less similar) because they both belong on the closer line
> of descent.
> -- Keith S. Thomson, _Living Fossil: the Story of the
> Coelacanth_. W.W. Norton & co., 1991. pp. 204-205
>
> Note how this distinguished former dean and CEO of "the Academy of
> Natural Sciences in Philadelphia" at the time of writing takes it
> for granted, in a book pitched at a general audience, that his
> readers will go along with a concept of "more closely related"
> that is so completely at variance with the usual layman's idea
> of close relationship.

Isn't it true that whatever meaning of the term you adopt the coelacanth
is more closely related to the cow than to the salmon? Unless by
"related" you mean "looks like". But you don't, do you?

> The trio of {{cow, *Elginerpeton*} , *Tiktaalik*} shows where
> that concept logically takes one. Did you look at the webpage
> I linked up there? The two latter would fit rather comfortably
> in the same Linnean order and probably family, and would thus
> be far more closely related than the first two, according to
> Fig. 1 in Romer's text.

Sure, if you adopt the horizontal classification that divides things up
at that point. But why that point? Isn't it an arbitrary point? Why is a
classification that unites those two taxa better than one that doesn't?
Why not consider the other taxa that could be united or separated by
some other arbitrary line?

Gross hyperbole. Also, I don't understand what I'm being unclear about.

Apparently, you haven't understood that this is problematic for your
argument in favor of horizontal classification. Your argument is that it
unites "closely related" species. And yet it arbitrarily unites some
species and arbitrarily separates others. What's the point of that?

>> Any classification that
>> splits the tree at any point must divide close relatives. It's a
>> physical impossibility to do otherwise. Thus the horizontal
>> classification doesn't have the advantage you suppose.
>
> I never supposed any such thing.

Then I don't understand why you brought up horizontal classification or
what you think its advantage is. Why did you bring it up, and what do
you think its advantage is?

To use Romer's tree, suppose that within Family B, say at the first x
above B', we place another fossil, B''. B'', by the definition of
"closest relative" you prefer, should be classified along with B',
right? And of course this could be repeated by adding incrementally new
taxa along the stem of Family B. Where should we put the line? Where
could we put the line that would be objectively better than putting it
below B', as in the left half of Fig. 1?

[delete gratuitous imputations of dementia]

>>> That's why I want to get to the bottom of what happened during
>>> the "cladist wars". I find it very hard to believe that none
>>> of the traditional systematists didn't press the issue of
>>> Romer's usage, and adopt it for their own.
>>
>> The usage of "related" is not really a big issue.
>
> It's a shame that the traditional systematists didn't make it one,
> unless they did, and history is being rewritten by the victors.

It's clearly not a big deal since Romer seems to use two definitions
without specifying when he's using one and when he's using the other.

>> And I will point out
>> again that Romer used it in two contradictory ways on the very page you
>> reference.

[snip gratuitous introduction of Marxism]

> You mean "two contrasting ways" or actually, "two ways that are
> different yet totally compatible with each other."

No, I mean two mutually incompatible ways. A horizontal classification
is incompatible with a vertical one. You can't classify the same taxa
both ways at once.

> I take it you are referring to the following in Fig. 1.
>
> [The vertical classification] makes clear the relation
> [*sic*: not "close relation"] of early ancestors (A' B')
> to their descendants but separates them sharply from C,
> the common ancestor, and other side branches, such as D,
> to which they are closely related.
>
> Note where the term "closely related" is used -- exactly the way
> it is used in human genealogies.

Word-lawyering. We aren't talking about the definition of "closely
related" but about "related" and "relation".

[snip a second gratuitous imputation of dementia]

[Oxyaena]

On 8/20/2018 4:13 PM, Peter Nyikos wrote:
> Oxyaena goes on libeling me below, copiously, despite minuscule
> provocation by me this time around.

By "little provocation" you mean "call Oxyaena mentally ill". I like how
you put "this time around", as well, a tacit admission to you flaming
me, despite your ill-founded protests to the contrary.

[snip bullshit]

> Woe unto them that call evil good, and good evil; that put
> darkness for light, and light for darkness... Isaiah 5:20
>
> The quotation from Charlemagne at the end also speaks to the difference
> between moral right and wrong, and you have been heedless of it for
> weeks now.

It's a little inappropriate to be taking the "moral" high ground now,
don't you think, Peter? After all, it *was* a mutual harangue wherein
you viciously libeled me and insulted me behind my back, such as below,
which hasn't been snipped so readers can see just how he insulted me.

[Oxyaena]

On 8/20/2018 3:43 PM, Peter Nyikos wrote:
> On Monday, August 20, 2018 at 12:23:16 PM UTC-4, Oxyaena wrote:
>> On 8/20/2018 11:14 AM, Peter Nyikos wrote:
>>> On Friday, August 17, 2018 at 9:33:35 PM UTC-4, John Harshman wrote:
>>>> On 8/17/18 5:59 PM, Peter Nyikos wrote:
>>>>> Finally, I get a halfway sincere and sane, and almost wholly on-topic,
>>>>> reply from Oxyaena!
>>>>>
>>>>> This will help me to decide just how to handle the request
>>>>> John made to both of us in a reply to Oxyaena (mild surprise: not
>>>>> to me).
>>>
>>> The mild surprise was occasioned by the fact that when Erik and I went
>>> at each other, your first reply was to me, and only the second such reply
>>> went to Erik after a wholly new phase of our being at loggerheads
>>> with each other.
>>>
>>>> Consider that request made right here, right now. Will that help?
>>>
>>> Gratuitous redundancy is never helpful. What would have been helpful
>>> would have been advice on how to go about disengaging myself, and
>>> what to do if Oxyaena doesn't follow suit. See my PS at the end.
>>>
>>

[snip trolling]

Clarify. How exactly does it do a better job than cladistics at this
issue? Romer's Fig 1 seems to be your escape hatch when confronted with
basic fucking questions about the pros and cons of Linnaean taxonomy, as
if you're incapable of answering them yourself.

>
>> *Elginerpeton* is a
>> sarcopterygian, a salmon is an actinopterygian,
>
> Even before last week, I criticized the choice of salmon even
> among extant organisms, by way of explaining how the
> traditional systematists really botched the choice of taxa -- if indeed
> it wasn't foisted on them by the cladophiles.

Can we agree to stop using that prejudiced term "cladophiles". There are
no such thing.

>
> You have some catching up to do here.

You still have yet to explain how Linnaean taxonomy does a better job at
this than cladistics. I`m still waiting. I would agree that they botched
the classification of Osteichthys by placing sarcopterygians and
actinopterygians in a single paraphyletic clade, while placing tetrapods
outside that clade, thereby giving the false impression that lungfish
are more closely related to salmon than cows.

>
>
> [snip harping on salmon, done later on the same page by
> Keith S. Thompson anyway]

Here's the section Nyikos conveniently, and dishonestly, snipped:

"the two clades diverged long before lungfish and *Elginopterpeton* came
about, and the genome of a lungfish therefore more closely resembles a
cow's genome than a salmon's genome. This doesn't even have to do with
the everyday meaning of the term "closely related", lungfish are more
closely related to cows than they are to salmon, irregardless of what
definition you use for the term "closely related". Linnaean taxonomy
falls apart when it comes to accurately showing phylogenetic
relationships, while cladistics does a better job at it."

How is that mere "harping" about salmon? Looks like I caught you, once
again, lying about what I had wrote. Care to address what I wrote, Nyikos?

>
>> Cue whining about how "cladophiles" co-opted the term "closely related".
>
> All these years, have you really missed my repeated skewering of this
> use of the word "whining"??

Still counts as whining.

[snip long off-topic diatribe]

>
>
>> that Harshman doesn't want to
>> talk about,
>
> Harshman has told me many times that my wants are of no
> interest. I don't even think he adds "to me" when he does this.
>
> Similarly, his wants are of no interest to me. Legitimate concerns
> are a different issue altogether.

Harshman doesn't want to talk about it with you, therefore, if you're
truly capable of acting like a civilized human being rather than a
barbarian, you should *respect* (a concept you seemingly have no
knowledge of) his wishes. There's something called "The Golden Rule" for
a reason, Nyikos.

>
>
>> you bringing it up again even after he asked you to stop
>
> Document where he did this concerning the above issues, or retract.

The fact that you just wrote above that "my wants are of no interest" is
more than sufficient for documentation purposes.

>
>>>>> That's why I want to get to the bottom of what happened during
>>>>> the "cladist wars". I find it very hard to believe that none
>>>>> of the traditional systematists didn't press the issue of
>>>>> Romer's usage, and adopt it for their own.
>>>>
>>>> The usage of "related" is not really a big issue.
>>>
>>> It's a shame that the traditional systematists didn't make it one,
>>> unless they did, and history is being rewritten by the victors.
>>>
>>>
>>>> And I will point out
>>>> again that Romer used it in two contradictory ways on the very page you
>>>> reference.
>>>
>>> I have never seen, before, anyone except Marxists use the word
>>> "contradiction" and its derivatives in the way you are using it here.
>>>
>>> [Not that I have anything against Marxists as a whole. There have
>>> been some very fine people among them, including IIRC Stephen Jay Gould.]
>>>
>>
>> "I`m not prejudiced, but..."
>
> Typical mindless leftist retort noted.

In other words, "I`m not prejudiced, but..."

>
> Besides, the bracketed aside was just to ward off the very
> sort of leftist harangue at which you are hinting.

So you think that saying that some Marxists were "good people" justifies
your bigotry towards Marxists? Dull surprise.

https://rationalwiki.org/wiki/I%27m_not_prejudiced,_but...

Try improving your reading comprehension and see why the above is a
logical fallacy.

>
>
>>
>>>
>>> Peter Nyikos
>>> Professor, Department of Mathematics -- standard disclaimer--
>>> University of South Carolina
>>> http://people.math.sc.edu
>>>
>>> PS. In lieu of any suggestions by you as to how to word it,
>>> I will announce my new policy on Oxyaena later today.
>>>
>>
>> I'll be glad to hear it, so I can finally be done with the burden of
>> having to address the libels you've written about me.
>
> That burden is nonexistent, as I documented in a post today
> where you libeled me with the charge that I had libeled you.
> What I had done instead was to thoroughly document a libel
> by you that originated in talk.origins and has been tenaciously adhered to
> both there and here in sci.bio.paleontology.

Bullshit. Just because planets were capable of forming six billion years
ago doesn't mean life was, and even if it was, it took over 4 billion
years for intelligent life to come about on Earth, and most of the
history of life on Earth life consisted solely of microbes. The 1.5
billion year span between when the universe settled down enough for
planets to form and when Earth formed isn't nearly enough time for
intelligent, or even multicellular, life to come about, let alone a
Kardashev Type II civilization capable of terraforming entire planets.

You have never demonstrated any ignorance on my part about abiogenesis,
and I have pointed this out to you multiple times. You'll probably snip
this like you always do, because it inconveniences you, so I'll repost
it every time you snip it. You libel me about my supposed ignorance on
abiogenesis, as I have pointed out multiple times. In short, you're a
two-faced sack of shit and you *know* it too.

>
> If you go on libeling me after I've announced my policy
> later today, don't expect me to correct you.
>
> Will that whet your appetite for further libels? Only time will tell.
>

It'll give me reason to stop responding to YOUR libels, and I
wholeheartedly welcome it, even though it doesn't signify any
significant change of heart on your behalf, most importantly an
admission of wrong doing, you'd rather pin all the blame on me as a
convenient scapegoat for the shit you've done.

>
>> Let's see if you
>> can hold up your promise.
>
> That knife cuts both ways.

Glad to see you tacitly admitting to the fact that you're at fault too.
See, isn't honesty great, Peter?

>
>
> Peter Nyikos
> Professor of Mathematics -- standard disclaimer--
> University of South Carolina
> http://www.math.sc.edu/~nyikos/
>

[Peter Nyikos]

On Monday, August 20, 2018 at 5:27:25 PM UTC-4, John Harshman wrote:
> On 8/20/18 8:14 AM, Peter Nyikos wrote:
> > On Friday, August 17, 2018 at 9:33:35 PM UTC-4, John Harshman wrote:
> >> On 8/17/18 5:59 PM, Peter Nyikos wrote:
> >>> Finally, I get a halfway sincere and sane, and almost wholly on-topic,
> >>> reply from Oxyaena!
> >>>
> >>> This will help me to decide just how to handle the request
> >>> John made to both of us in a reply to Oxyaena (mild surprise: not
> >>> to me).
> >
> > The mild surprise was occasioned by the fact that when Erik and I went
> > at each other, your first reply was to me, and only the second such reply
> > went to Erik after a wholly new phase of our being at loggerheads
> > with each other.
> >
> >> Consider that request made right here, right now. Will that help?
> >
> > Gratuitous redundancy is never helpful. What would have been helpful
> > would have been advice on how to go about disengaging myself, and
> > what to do if Oxyaena doesn't follow suit. See my PS at the end.
>
> That too seems simple enough:

Seems, to you. But I've had more experience in these matters
than yourself.

> don't respond to insults or don't respond
> to posts containing insults;

And shut off all on-topic discussion with Oxyaena, who is
far more proactive and detailed in such discussions with you?
Not in s.b.p.

My policy has to do with statements:

Beginning as of the appearance of this post, and for the rest of this
week, I will only reply to on-topic statements [1] by Oxyaena that
are devoid of denigratory personal comments.

[1]i.e., in paleontology and systematics, the latter for the convenience
of Harshman -- giganews does not support sci.bio.systematics.

This is more tricky than it sounds. Just where does one draw the line
at documentably false on-topic statements that give a highly distorted
picture of my competence?

https://groups.google.com/d/msg/sci.bio.paleontology/temctjrIx0Q/gafjAWDoCQAJ
Date: Mon, 20 Aug 2018 19:22:45 -0700 (PDT)
Message-ID: <20ab638d-1cce-47ed...@googlegroups.com>
Subject: OT: Partial Moratorium On Replies to Oxyaena

In it, I linked a post which illustrates the difficulty of drawing
that sort of line. The only place where I think your kind of policy
works was given at the end of the post I've linked here:

[2] On the other hand, off-topic derogatory personal
remarks will be snipped without marking the snip.

> don't indulge in insults yourself.

That is almost a corollary of the policy: I don't want to make
my weeding out of derogatory personal statements any harder
than it already is.

Your two-word retort is very helpful to me. It enables me to discount all
comments by you on the "cladist wars" unless they are accompanied
by documentation. ["discount" does not mean "ignore": I might
ask further questions whose answers you may be able to document.]

> > At a now-famous meeting of vertebrate zoologists
> > [*sic*: not "paleontologists"]
> > in Reading, England, in 1978, the zoological conundrum
> > about the lungfish, the salmon, and the cow caused a mild
> > sensation. In retrospect it should not have caused more
> > than a blink of the eye. The most obvious answer is,
> > of course, that the two fishes *appear* to be more closely
> > related than either is to a cow. Both are fishes, after all.
> > But ... blink the eye, and it is evident that the lungfish
> > and the cow are more closely *related* (although physically
> > less similar) because they both belong on the closer line
> > of descent.
> > -- Keith S. Thomson, _Living Fossil: the Story of the
> > Coelacanth_. W.W. Norton & co., 1991. pp. 204-205
> >
> > Note how this distinguished former dean and CEO of "the Academy of
> > Natural Sciences in Philadelphia" at the time of writing takes it
> > for granted, in a book pitched at a general audience, that his
> > readers will go along with a concept of "more closely related"
> > that is so completely at variance with the usual layman's idea
> > of close relationship.
>
> Isn't it true that whatever meaning of the term you adopt the coelacanth
> is more closely related to the cow than to the salmon?

That's exactly why I said the example was so poorly chosen by
the traditional systematists -- unless it was foisted on
them by the cladophiles.

> Unless by
> "related" you mean "looks like". But you don't, do you?

As you've known for the last 7.6 years, or maybe longer if
you remember my posts to s.b.p. in the six years starting
with 1995, the answer is Yes.

>
> > The trio of {{cow, *Elginerpeton*} , *Tiktaalik*} shows where
> > that concept logically takes one. Did you look at the webpage
> > I linked up there? The two latter would fit rather comfortably
> > in the same Linnean order and probably family, and would thus
> > be far more closely related than the first two, according to
> > Fig. 1 in Romer's text.
>
> Sure, if you adopt the horizontal classification that divides things up
> at that point. But why that point? Isn't it an arbitrary point?

Yes, but we are human beings, not automatons, and such divisions
are extremely helpful in gauging relationships *sensu* Romer.

> Why is a
> classification that unites those two taxa better than one that doesn't?

*Elginerpeton* and *Bos*? They ARE united, but in a titanic clade that
could best be termed an "infraphylum". Which is the best that any
reasonable classification can do for them.

> Why not consider the other taxa that could be united or separated by
> some other arbitrary line?

Back around 1998 I floated a system that does that, and Erik somehow
remembers it although I have no recollection of him posting before
2010. But I knew that cladists would never abandon their vertical
classification, and I saw that I would have my hands full just trying to
support a side-by-side use of both existing systems.

> > More about Fig. 1 below.
> >
> > As I was saying earlier:
> >
> >>>>>>> Worse yet, they either did not know how Romer 1945 used the term
> >>>>>>> "closely related " in a completely different way than the
> >>>>>>> way I've seen it used in every account I've seen so far,
> >>>>>>> or else we have another example of "history is written by the victors."
> >>>>>>>
> >>>>>>> That reminds me: did you see whether the 1966 edition has something
> >>>>>>> fitting the description I gave you of Fig. 1 of the 1945 edition
> >>>>>>> in a post of yesterday? You haven't replied to that post yet.
> >>>>>>
> >>>>>> Yes, I saw it, and I suspect the text didn't change either. To the
> >>>>>> extent Romer's text contains an argument for paraphyly, that argument is
> >>>>>> seriously flawed.

You were being very unclear here, in the same way in which I
point out near the end.

> >>>>> I see you are tenaciously clinging to your lack of support for
> >>>>> "no, no, no, and no," and even for provocative comments like
> >>>>> the one you've just made, which would at least initiate a support
> >>>>> for one or more "no"s.
> >>>>>
> >>>>> On the other hand, I begin to support a Yes answer to 2. later
> >>>>> in this post.
> >>>>>
> >>>>>
> >>>>>> Ironically, the inclusion of fossils makes it more
> >>>>>> flawed than if he had considered only extant species.
> >>>>>
> >>>>> I think the opposite is true, and I'll explain in detail when
> >>>>> I have more time to spare. Meanwhile, your tenacious clinging
> >>>>> to your policy is exacerbated by the leading word "Ironically."
> >>>>>
> >>>>
> >>>> Why?
> >
> > Because you are being less clear in the last two things you
> > wrote in that earlier reply, than I have ever been about anything
> > in the 7+ years we've argued in talk.origins and s.b.p. -- your
> > "exhortations" to me to be "more clear" notwithstanding.
> >
> > And you seem perfectly content to stay that way.
>
> Gross hyperbole.

I don't see how. Please explain.

> Also, I don't understand what I'm being unclear about.

The reasons for your blatant assertion. And for the word "Ironically"
which accompanies it.


In my next reply to this post, I'll pick up where I left off here.


Peter Nyikos

[John Harshman]

On 8/22/18 10:05 AM, Peter Nyikos wrote:
>>> Your ignorance of this debate makes me wonder just how fragmentary
>>> your knowledge of the "cladist wars" actually is.
>>
>> Not helpful.
>
> Your two-word retort is very helpful to me. It enables me to discount all
> comments by you on the "cladist wars" unless they are accompanied
> by documentation. ["discount" does not mean "ignore": I might
> ask further questions whose answers you may be able to document.]

Wow, that's a lot to get from two words. Now in fact the cladist wars
(probably a bad term) happened mostly in the '70s and '80s, but were
still sputtering while I was an undergrad, and were almost entirely over
by the time I reached graduate school. Still, I encountered some bits
and pieces of them. They came later to ornithology than to some other
disciplines, which allowed me more experience than I would have had if I
were in ichthyology, where the initial battles happened. By the time I
was really active, the pheneticists and the "evolutionary" systematists
had mostly died, retired, or been converted. The live battle was between
the fundamentalist cladists (Hennig Society) and the less doctrinaire
mainstream, over likelihood methods, bootstrapping, explicit models, and
such.

And I have read much more of the actual literature that made up the
cladist wars than you have, and know more about the actual issues
involved than you do. Whatever this "now-famous meeting" may be, and
whatever was the crucial point about cows and fish, they're not the
shibboleth you suppose.

The example was only poorly chosen if the controversy was over the
meaning of "closely related". But it wasn't. The "evolutionary"
systematists wanted to represent both cladistic relationships and
morphological similarity in their classifications, and the controversy
in systematics had little to do with fossils or your favored definition
of "relationship". That's why extant species were used and why those
species could represent the controversy even though your idea of
"relationship" would result in the same classification as a cladistic idea.

>> Unless by
>> "related" you mean "looks like". But you don't, do you?
>
> As you've known for the last 7.6 years, or maybe longer if
> you remember my posts to s.b.p. in the six years starting
> with 1995, the answer is Yes.

In that respect, you differ from the "evolutionary" systematists,
particularly as represented by Ernst Mayr.

>>> The trio of {{cow, *Elginerpeton*} , *Tiktaalik*} shows where
>>> that concept logically takes one. Did you look at the webpage
>>> I linked up there? The two latter would fit rather comfortably
>>> in the same Linnean order and probably family, and would thus
>>> be far more closely related than the first two, according to
>>> Fig. 1 in Romer's text.
>>
>> Sure, if you adopt the horizontal classification that divides things up
>> at that point. But why that point? Isn't it an arbitrary point?
>
> Yes, but we are human beings, not automatons, and such divisions
> are extremely helpful in gauging relationships *sensu* Romer.

But they aren't. That's my point. Species close together on opposite
sides of that arbitrary line will be separated, and so the divisions
will not be helpful in gauging their relationships sensu Romer.

>> Why is a
>> classification that unites those two taxa better than one that doesn't?
>
> *Elginerpeton* and *Bos*? They ARE united, but in a titanic clade that
> could best be termed an "infraphylum". Which is the best that any
> reasonable classification can do for them.

No, Elginerpeton and Tiktaalik.

>> Why not consider the other taxa that could be united or separated by
>> some other arbitrary line?
>
> Back around 1998 I floated a system that does that, and Erik somehow
> remembers it although I have no recollection of him posting before
> 2010. But I knew that cladists would never abandon their vertical
> classification, and I saw that I would have my hands full just trying to
> support a side-by-side use of both existing systems.

Are you talking about your overlapping-taxa proposal? Yes, we should
definitely ignore that if so. But you are not addressing the question.
That proposal won't fly, and should not. Given that you are limited to
disjunct taxa, how do you deal with the question?

>>> More about Fig. 1 below.
>>>
>>> As I was saying earlier:
>>>
>>>>>>>>> Worse yet, they either did not know how Romer 1945 used the term
>>>>>>>>> "closely related " in a completely different way than the
>>>>>>>>> way I've seen it used in every account I've seen so far,
>>>>>>>>> or else we have another example of "history is written by the victors."
>>>>>>>>>
>>>>>>>>> That reminds me: did you see whether the 1966 edition has something
>>>>>>>>> fitting the description I gave you of Fig. 1 of the 1945 edition
>>>>>>>>> in a post of yesterday? You haven't replied to that post yet.
>>>>>>>>
>>>>>>>> Yes, I saw it, and I suspect the text didn't change either. To the
>>>>>>>> extent Romer's text contains an argument for paraphyly, that argument is
>>>>>>>> seriously flawed.
>
> You were being very unclear here, in the same way in which I
> point out near the end.

Have I clarified? It's all about that arbitrary line. Horizontal
classifications are no better at putting similar species into the same
category than vertical ones are. They will both be likely to separate
similar species, except in conveniently designed artificial examples.

>>>>>>> I see you are tenaciously clinging to your lack of support for
>>>>>>> "no, no, no, and no," and even for provocative comments like
>>>>>>> the one you've just made, which would at least initiate a support
>>>>>>> for one or more "no"s.
>>>>>>>
>>>>>>> On the other hand, I begin to support a Yes answer to 2. later
>>>>>>> in this post.
>>>>>>>
>>>>>>>
>>>>>>>> Ironically, the inclusion of fossils makes it more
>>>>>>>> flawed than if he had considered only extant species.
>>>>>>>
>>>>>>> I think the opposite is true, and I'll explain in detail when
>>>>>>> I have more time to spare. Meanwhile, your tenacious clinging
>>>>>>> to your policy is exacerbated by the leading word "Ironically."
>>>>>>>
>>>>>>
>>>>>> Why?
>>>
>>> Because you are being less clear in the last two things you
>>> wrote in that earlier reply, than I have ever been about anything
>>> in the 7+ years we've argued in talk.origins and s.b.p. -- your
>>> "exhortations" to me to be "more clear" notwithstanding.
>>>
>>> And you seem perfectly content to stay that way.
>>
>> Gross hyperbole.
>
> I don't see how. Please explain.

No. It's a matter of opinion. But it's just the sort of pointless attack
that you could easily avoid. Just tell me I'm being unclear. No need to
characterize the extent of my unclarity or compare it unfavorably with
your own.

>> Also, I don't understand what I'm being unclear about.
>
> The reasons for your blatant assertion. And for the word "Ironically"
> which accompanies it.

Simple: extant groups (i.e. groups for which we ignore all but extant
species) have been pruned enough that there are often convenient gaps in
morphology at which one may place the boundaries of paraphyletic groups
without separating similar species. (I would argue that there are
problems here too, essentially that this depends greatly on which
characters we choose to see, but that's another argument.) But if we
include fossils, many of those gaps go away, and we are left with that
arbitrary line separating similar species on both sides. Further, even
if there's a gap now, at any time we may find a fossil that fills that
gap. That's why the irony: the problems with horizontal classification
are greater if you consider fossils than if you don't.

Did that explain clearly enough?

[Peter Nyikos]

I don't believe you've ever answered this question, Oxyaena.
Am I wrong?

Wrong question. It does a much needed job that cladistic classification
does not, while cladistic classification does a much needed job that
the traditional does not. It is only the two together that give a
really accurate picture of life on earth through the eons to anyone who
doesn't want to make poring over cladograms into a lifelong obsession.

That's what I meant by "the equally one-sided contribution of
cladistic systematics." Note especially the word "equally".
[Yes, I should have written "classification" instead of "systematics."
My bad.]

>
> >> *Elginerpeton* is a
> >> sarcopterygian, a salmon is an actinopterygian,
> >
> > Even before last week, I criticized the choice of salmon even
> > among extant organisms, by way of explaining how the
> > traditional systematists really botched the choice of taxa -- if indeed
> > it wasn't foisted on them by the cladophiles.
>
> Can we agree to stop using that prejudiced term "cladophiles".

There is nothing prejudiced about a term that describes something
all of you are proud of: your love of clades to the point of
disapproving of any alternative method of classification, including
the evolution-based system that Linnean classification had become
by the beginning of the 20th century.

> There are no such thing.

There most assuredly is such a thing, and I've defined it again
for you since your memory seems to be as bad as that of John Harshman.

The *word* is my own coinage, and as a self-explanatory a word as
any in systematics, and more self-explanatory than many.

> >
> > You have some catching up to do here.
>
> You still have yet to explain how Linnaean taxonomy does a better job at
> this than cladistics. I`m still waiting. I would agree that they botched
> the classification of Osteichthys by placing sarcopterygians and
> actinopterygians in a single paraphyletic clade, while placing tetrapods
> outside that clade, thereby giving the false impression that lungfish
> are more closely related to salmon than cows.

> > [snip harping on salmon, done later on the same page by
> > Keith S. Thompson anyway]
>

> Here's the section [that was] snipped:

>
> "the two clades diverged long before lungfish and *Elginopterpeton* came
> about, and the genome of a lungfish therefore more closely resembles a
> cow's genome than a salmon's genome. This doesn't even have to do with
> the everyday meaning of the term "closely related", lungfish are more
> closely related to cows than they are to salmon, irregardless of what
> definition you use for the term "closely related". Linnaean taxonomy
> falls apart when it comes to accurately showing phylogenetic
> relationships, while cladistics does a better job at it."
>
> How is that mere "harping" about salmon?

Two ways, which supplement each other to make the picture complete.

1. You are ignoring my words I wrote above:

[reposted from above:]

> > Even before last week, I criticized the choice of salmon even
> > among extant organisms, by way of explaining how the
> > traditional systematists really botched the choice of taxa -- if indeed
> > it wasn't foisted on them by the cladophiles.

[end of repost]

2. Your last sentence is about a theme that has already been beaten
to death: the cladophile definition of "phylogenetic relationships"
that banishes the topic of "ancestral genus - closely descendant genus"
topic to from the realm of science.

> >> Cue whining about how "cladophiles" co-opted the term "closely related".

Actually, they didn't. Even Keith S. Thompson slipped up on page 43
and used "closely related" in the way Romer uses it in Fig. 1.
That's the ONLY example I know of a doctrinaire cladistic systematist
ever using the term "closely related." Once you get beyond "sister group" [1]
it loses meaning.

[1] Every time that term is used, it is vital to ask: among extant
organisms, or all known organisms? The difference can be
enormous, as in "the sister group of the clade determined
by Ornithorhychus and Tachyglossus".

> >> that Harshman doesn't want to
> >> talk about,
> >
> > Harshman has told me many times that my wants are of no
> > interest. I don't even think he adds "to me" when he does this.
> >
> > Similarly, his wants are of no interest to me. Legitimate concerns
> > are a different issue altogether.
>
> Harshman doesn't want to talk about it with you, therefore,

...he has just as much right to want this as he does to be
snarky with you. [2] And I have just as much right to go
on talking about it as long as I don't violate our 4+ year
agreement. There's been a lot of pushing of the envelope on
that one by him (and sometimes me) but it remains intact
between him and me.

[2] I am referring to your complaint about his treatment of your OP in the
thread, "Were pterosaurs bipedal?" After all, you can't accuse John of a
violation of an agreement that you never had with him.


Remainder deleted, to be replied to later. Duty calls.


Peter Nyikos

[Oxyaena]

Wrong about what? Have I read about the "cladist wars"? Yes, I have. Do
I have any interest in discussing them? No, I don't.

You paint me in with Harshman when I have pointed out to you multiple
times I am not a "cladophile", I believe cladistics should be reformed
but I don't think Linnaean taxonomy is the way to do it.

>
>
>> There are no such thing.
>
> There most assuredly is such a thing, and I've defined it again
> for you since your memory seems to be as bad as that of John Harshman.

Don't insult my memory, it makes you look childish and hypocritical (not
that you aren't a hypocrite, IMHO). I have an eidetic memory, I just
disagree with you that the term "cladophile" is a non-prejudicial term.

>
> The *word* is my own coinage, and as a self-explanatory a word as
> any in systematics, and more self-explanatory than many.

Bullshit, it implies that the vast majority of systematists have an
irrational obsession with cladistics. By your logic, my term
"cladophobe" is just as accurate.

So you're saying that your mother is more closely related to your
grandmother than to you. Perfect logic. The genome of the lungfish is
closer to a cow's genome than to a salmon's genome, so therefore by all
rights dipnoi is the sister group to Tetrapodomorpha. Salmon don't even
fall in there outside of them being "fish". Try comparing a lungfish's
fin and a salmon's fin and see how different they are, the structure of
the fin of the lungfish is closer to the limb of a tetrapod than that of
a salmon's fin, so in this case there's no justification for placing
lungfish with salmon in one taxon and cows in another taxon, it's
completely arbitrary.

>
>
>
>>>> Cue whining about how "cladophiles" co-opted the term "closely related".
>

[snip whining]

>
> [1] Every time that term is used, it is vital to ask: among extant
> organisms, or all known organisms? The difference can be
> enormous, as in "the sister group of the clade determined
> by Ornithorhychus and Tachyglossus".

Again, we have no DNA from most fossil organisms, so it is better to us
extant organisms to classify clades than extinct ones because of the
lack of DNA with fossils over a million years old.

>
>
>>>> that Harshman doesn't want to
>>>> talk about,
>>>
>>> Harshman has told me many times that my wants are of no
>>> interest. I don't even think he adds "to me" when he does this.
>>>
>>> Similarly, his wants are of no interest to me. Legitimate concerns
>>> are a different issue altogether.
>>
>> Harshman doesn't want to talk about it with you, therefore,

[snip irrelevancies]

[John Harshman]

On 8/23/18 8:54 AM, Oxyaena wrote:
> I believe cladistics should be reformed
> but I don't think Linnaean taxonomy is the way to do it.

Why do you think cladistics should be reformed and what do you think is
the way to do it?

[John Harshman]

On 8/23/18 8:54 AM, Oxyaena wrote:

> So you're saying that your mother is more closely related to your
> grandmother than to you. Perfect logic. The genome of the lungfish is
> closer to a cow's genome than to a salmon's genome, so therefore by all
> rights dipnoi is the sister group to Tetrapodomorpha.

Are you sure that the genomic distance is as you say? Even if it is,
that doesn't mean that relationships are properly judged by genetic
distance. That would hold only if there were a perfect molecular clock.
It could very well be (I have no idea) that both salmon and lungfish
have a slow rate of molecular evolution while cows have a fast rate, and
thus lungfish would be closer (by raw distance) to salmon than to cow.

> Salmon don't even
> fall in there outside of them being "fish". Try comparing a lungfish's
> fin and a salmon's fin and see how different they are, the structure of
> the fin of the lungfish is closer to the limb of a tetrapod than that of
> a salmon's fin, so in this case there's no justification for placing
> lungfish with salmon in one taxon and cows in another taxon, it's
> completely arbitrary.

Note that this is a valid statement only if the similarities of lungfish
fins and cow limbs are synapomorphies. If they're plesiomorphies,
nothing is implied about relationships.

I think your point is that there's no justification for a "fish" taxon
other than overall similarity, which even Peter rejects as a criterion,
and which is probably not even true if you look closely enough at
characters.

[Peter Nyikos]

On Monday, August 20, 2018 at 5:27:25 PM UTC-4, John Harshman wrote:
> On 8/20/18 8:14 AM, Peter Nyikos wrote:
> > On Friday, August 17, 2018 at 9:33:35 PM UTC-4, John Harshman wrote:
> >> On 8/17/18 5:59 PM, Peter Nyikos wrote:

Picking up where I left off in my first reply to your post:

[to Oxyaena:]

I don't know where you got this idea, in the wake of all my
harping on the fact that I want both the cladistic (vertical)
and the horizontal modern Linnean system to be developed and used.

What YOU don't seem to see is that the cladistic system also
separates taxa from each other in the same way, taxa that
are closely related by Romer's usage. It separates the cow
and Elginerpeton both equally from Tiktaalik, for instance.
And it separates Equus and Eohippus both equally from Hyracotherium --
which is so close to Eohippus by every criterion except
clade membership that it was LONG taken to be synonymous with Eohippus!

> Your argument is that it
> unites "closely related" species. And yet it arbitrarily unites some
> species and arbitrarily separates others. What's the point of that?

The point is easily seen in Perissodactyla. Even if the Linnean
system DID separate Eohippus and Hyracotherium from the rest of
Equioidea, one could see that the rest is a family contiguous
with the family "Eohippidae" and therefore the members of the
two families together would only amount to a superfamily.

The latter family would probably include all of Palaeotheridae
and Hyrachius and some very primitive tapirs, but it's a nice
compact family for all that. And it would be contiguous with
the rhinoceros and tapir families, and so the whole kit and
caboodle would be a superfamily.

If the Linnean system were allowed to evolve naturally,
with its researchers not shut out of governmental grant money
and out of positions at prestigious universities, the system
would evolve more and more towards a system like a giant
jigsaw puzzle with each new paleontological discovery.

Contiguous sets of pieces could be the subject
of essays on what the animals in each set have in common, and
how one might identify an animal as belonging in one set or
the other. Just as is the case with un-named, unranked clades.

Does you wife like jigsaw puzzles? Maybe she could explain
to you the merits of having a system like that, if the answer is Yes.
Or if she likes quilts, that could be helpful too.

>
> >> Any classification that
> >> splits the tree at any point must divide close relatives. It's a
> >> physical impossibility to do otherwise. Thus the horizontal
> >> classification doesn't have the advantage you suppose.
> >
> > I never supposed any such thing.
>
> Then I don't understand why you brought up horizontal classification or
> what you think its advantage is.

The advantages are the contributions they make to our understanding.
I wish you would stop assuming that I think horizontal classifications
are superior to vertical ones. I never did.

And now, maybe you can see why I objected to the wording of

1. Can paraphyletic groups be more useful in classification
than strict adherence to monophyly?

It seems my initial answer still hasn't sunk in:

Poorly worded. Ever since 2002 all I have ever argued for was for
cladophiles like you not to ban paraphyletic groups, but to admit
them side by side with monophyletic ones, because they also
contribute to our understanding of evolution.

> Why did you bring it up, and what do
> you think its advantage is?

I hope all the above helps. If it doesn't, please don't come up
with condescending retorts like "Please stop hinting and say
clearly what you mean." Try to figure out WHAT it is that you
find unclear.

> To use Romer's tree, suppose that within Family B, say at the first x
> above B', we place another fossil, B''. B'', by the definition of
> "closest relative" you prefer, should be classified along with B',
> right?

I don't do windows, and I don't do "closest relative." I do
use "close relative" in various senses. Have you still not
figured out that "members of the same Family" is Romer's
*ad hoc* definition of "closely related" in Fig 1.?

All things are relative. You are far from me when the issue
is walking from my place to yours. You are close to me
when we are talking about astronomical units.


Concluded in next reply, which will include a bit of the above
for context.


Peter Nyikos

Professor, Department of Math. -- standard disclaimer --

U. of South Carolina in Columbia
http://www.math.sc.edu/~nyikos/

[Oxyaena]

I believe that cladists sometimes redefine clades when there's no need
to do so, as they did by restricting Aves to only consist of members of
Neornithes, while other enantiornithines fit all of the characteristics
of birds, except for the possession of teeth (*Confuciusornis* doesn't
have teeth, but I think that's simply a matter of convergence rather
than shared synapomorphy between *Confuciusornis* and neornithines). In
other words, why reinvent the wheel?

I don't believe that cladistics should be wholesale replaced, and unlike
Peter I recognize that Linnaean taxonomy is out-dated, and fails to
accurately represent evolutionary relationships. I only propose minor
tweaks to the PhyloCode rather than outright replacing cladistics, which
is why I said "reform" rather than "replace", which is what Peter wants
to do.

Under the current rules of cladistics is the redefining of the clade
"Aves" valid? Yes, it was. Was it necessary? No, I don't think it was.
Of course, your mileage may vary.

[Oxyaena]

On 8/23/2018 12:15 PM, John Harshman wrote:
> On 8/23/18 8:54 AM, Oxyaena wrote:
>> So you're saying that your mother is more closely related to your
>> grandmother than to you. Perfect logic. The genome of the lungfish is
>> closer to a cow's genome than to a salmon's genome, so therefore by
>> all rights dipnoi is the sister group to Tetrapodomorpha.
>
> Are you sure that the genomic distance is as you say? Even if it is,
> that doesn't mean that relationships are properly judged by genetic
> distance. That would hold only if there were a perfect molecular clock.
> It could very well be (I have no idea) that both salmon and lungfish
> have a slow rate of molecular evolution while cows have a fast rate, and
> thus lungfish would be closer (by raw distance) to salmon than to cow.
>

Reasonably sure, since both lungfish and cows are sarcopterygians,
there's bound to be more similarities in the genome of both taxa than
either share with salmon. I haven't looked at the genomes of lungfish so
I'm only hypothesizing that the genomes of both lungfish and cows are
more similar to each other than either is to a salmon's genome based
upon the fact that dipnoi are the sister group to Tetrapodamorpha, and
salmon aren't even sarcopterygians, they're actinopterygians.

>> Salmon don't even fall in there outside of them being "fish". Try
>> comparing a lungfish's fin and a salmon's fin and see how different
>> they are, the structure of the fin of the lungfish is closer to the
>> limb of a tetrapod than that of a salmon's fin, so in this case
>> there's no justification for placing lungfish with salmon in one taxon
>> and cows in another taxon, it's completely arbitrary.
>
> Note that this is a valid statement only if the similarities of lungfish
> fins and cow limbs are synapomorphies. If they're plesiomorphies,
> nothing is implied about relationships.

Of course they are synapomorphies, no other organism outside of
Sarcopterygia possesses a humerus, while coelocanths, lungfish, and cows do.

>
> I think your point is that there's no justification for a "fish" taxon
> other than overall similarity, which even Peter rejects as a criterion,
> and which is probably not even true if you look closely enough at
> characters.

Partially true, my point is is that the "justification" for placing both
in a "fish" taxon is because humans label both lungfish and salmon as
"fish" without regards for the actual evolutionary history of both
clades, so it would at best be paraphyletic (a "fish" being any
vertebrate outside of Stegacophalia), and you and I both share the same
opinion about the validity of paraphyletic taxa.

[Peter Nyikos]

On Thursday, August 23, 2018 at 12:15:18 PM UTC-4, John Harshman wrote:
> On 8/23/18 8:54 AM, Oxyaena wrote:
> > So you're saying that your mother is more closely related to your
> > grandmother than to you.

I never said anything like that, because it flies in the face
of the ordinary meaning of "closely related" in family trees,
and I want any horizontal classification to get as close to
the everyday meaning as possible.

I HAVE said it is ridiculous to claim that Mitochondrial Eve
is more closely related to us than to her own mother (or sister,
if she had one) which would be the case if the cladistic
Procrustean-bed definition of "closely related" were adopted
by genealogists of family trees.

> > The genome of the lungfish is
> > closer to a cow's genome than to a salmon's genome, so therefore by all
> > rights dipnoi is the sister group to Tetrapodomorpha.
>
> Are you sure that the genomic distance is as you say? Even if it is,
> that doesn't mean that relationships are properly judged by genetic
> distance. That would hold only if there were a perfect molecular clock.
> It could very well be (I have no idea) that both salmon and lungfish
> have a slow rate of molecular evolution while cows have a fast rate, and
> thus lungfish would be closer (by raw distance) to salmon than to cow.

Apropos of "genomic distance," here is something I posted back in
April to sci.anthropology.paleo:

_____________________ begin included OP _________________________

In his 2015 book, _The Story of Life in 25 Fossils_, ungulate paleontologist
Donald Prothero gets sloppy when talking about other orders of mammals and
other classes of vertebrates. One example of sloppiness is his use, on pp.
329-331 of mere mitochondrial data to show genetic distance between various
groups (including some populations) in the clade {orangutan, human} of
hominoids.

Mitochondrial estimates of genetic distance are highly unreliable.
A notorious example is their "support" of the marsupionta hypothesis,
which claims that placental mammals and monotremes are more closely
related to each other than either is to marsupials (!)

All through the text, Prothero claims various results about distances
between humans and chimps, between chimps of different populations,
between lions and tigers, on "the DNA," even saying:

Our DNA is more similar to that of the two species of chimp
than the DNA of any two species of frog are similar to each other...

It is only in the caption of Figure 24.2 that [we learn that] the claims about DNA
apply only to mitochondrial DNA. The source for this is rather old:


Pascal Gagneux et. al., "Mitochondrial Sequences Show Diverse
Evolutionary Histories of African Hominoids," PNAS 93 (1999), Fig. 1B.


Does anyone reading this know of any studies of genetic distance
between some of these groups, based on genomic DNA? preferably,
a sizable chunk of it!


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

================== end of OP for thread archived st:
https://groups.google.com/forum/#!activity/sci.anthropology.paleo/CwjBLigSEAAJ/sci.anthropology.paleo/M47pc-CYZj4/cKVsSsmBBQAJ


This occasioned some lively debate, but no one could answer
the question at the end. Can you answer it, John? How about
other readers? [Never mind the "of these" in "some of these groups"]

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --
U. of South Carolina

http://www.math.sc.edu/~nyikos/

[John Harshman]

Well, there are no current rules of cladistics. Even the PhyloCode is
just an attempted standard. The code does say that the first valid
phylogenetic definition of a clade (published after some date that I
forget) has priority over later definitions. I'm not sure there has been
a properly published definition for Aves.

Now, I happen to like crown group definitions, and even prefer the crown
group definition of Aves. We could argue about that if you liked. But I
wouldn't consider that to rise to the level of "cladistics should be
reformed".

[John Harshman]

On 8/23/18 11:08 AM, Oxyaena wrote:
> On 8/23/2018 12:15 PM, John Harshman wrote:
>> On 8/23/18 8:54 AM, Oxyaena wrote:
>>> So you're saying that your mother is more closely related to your
>>> grandmother than to you. Perfect logic. The genome of the lungfish is
>>> closer to a cow's genome than to a salmon's genome, so therefore by
>>> all rights dipnoi is the sister group to Tetrapodomorpha.
>>
>> Are you sure that the genomic distance is as you say? Even if it is,
>> that doesn't mean that relationships are properly judged by genetic
>> distance. That would hold only if there were a perfect molecular clock.
>> It could very well be (I have no idea) that both salmon and lungfish
>> have a slow rate of molecular evolution while cows have a fast rate, and
>> thus lungfish would be closer (by raw distance) to salmon than to cow.
>>
>
> Reasonably sure, since both lungfish and cows are sarcopterygians,
> there's bound to be more similarities in the genome of both taxa than
> either share with salmon.

That's not a valid assumption. As I've said, it assumes a perfect
molecular clock, and no such clock exists.

> I haven't looked at the genomes of lungfish so
> I'm only hypothesizing that the genomes of both lungfish and cows are
> more similar to each other than either is to a salmon's genome based
> upon the fact that dipnoi are the sister group to Tetrapodamorpha, and
> salmon aren't even sarcopterygians, they're actinopterygians.

You are correct in the relationships, but you're incorrect in supposing
that the relationships assure genomic similarity.

>>> Salmon don't even fall in there outside of them being "fish". Try
>>> comparing a lungfish's fin and a salmon's fin and see how different
>>> they are, the structure of the fin of the lungfish is closer to the
>>> limb of a tetrapod than that of a salmon's fin, so in this case
>>> there's no justification for placing lungfish with salmon in one taxon
>>> and cows in another taxon, it's completely arbitrary.
>>
>> Note that this is a valid statement only if the similarities of lungfish
>> fins and cow limbs are synapomorphies. If they're plesiomorphies,
>> nothing is implied about relationships.
>
> Of course they are synapomorphies, no other organism outside of
> Sarcopterygia possesses a humerus, while coelocanths, lungfish, and cows
> do.

My point there is that mere similarity doesn't count; only
synapomorphies count.

[John Harshman]

You are confusing genetic distance with phylogenetic relationships.
Mitochondrial DNA can be used as a perfectly good estimate of genetic
distance, and that has nothing to do with whether it's useful for all
phylogenetic questions.

> All through the text, Prothero claims various results about distances
> between humans and chimps, between chimps of different populations,
> between lions and tigers, on "the DNA," even saying:
>
> Our DNA is more similar to that of the two species of chimp
> than the DNA of any two species of frog are similar to each other...
>
> It is only in the caption of Figure 24.2 that [we learn that] the claims about DNA
> apply only to mitochondrial DNA. The source for this is rather old:
>
> Pascal Gagneux et. al., "Mitochondrial Sequences Show Diverse
> Evolutionary Histories of African Hominoids," PNAS 93 (1999), Fig. 1B.
>
> Does anyone reading this know of any studies of genetic distance
> between some of these groups, based on genomic DNA? preferably,
> a sizable chunk of it!

Yes. There are quite a few. But there's no problem with anything you
quote Prothero saying or with using mtDNA to estimate genetic distances
or with using a publication from 1999.

> ================== end of OP for thread archived st:
> https://groups.google.com/forum/#!activity/sci.anthropology.paleo/CwjBLigSEAAJ/sci.anthropology.paleo/M47pc-CYZj4/cKVsSsmBBQAJ
>
>
> This occasioned some lively debate, but no one could answer
> the question at the end. Can you answer it, John? How about
> other readers? [Never mind the "of these" in "some of these groups"]

This is the sort of thing you should easily be able to google. Have you
tried? For a whole-genome comparison, try The Chimpanzee Sequencing and
Analysis Consortium. Initial sequence of the chimpanzee genome and
comparison with the human genome. Nature 2005; 437:69-87.

[John Harshman]

Irrelevant. It's problematic for the acceptance of paraphyletic groups,
whether or not you think clades are fine too.

> What YOU don't seem to see is that the cladistic system also
> separates taxa from each other in the same way, taxa that
> are closely related by Romer's usage.

Of course it does. The cladistic system doesn't attempt not to separate
similar-looking taxa. Similarity is not what cladistic classification is
about. It attempts to recognize only cladistic relationships. Trying to
represent both similarity and cladistic relationships in a single
classification is doomed to failure, which is why it shouldn't be attempted.

> It separates the cow
> and Elginerpeton both equally from Tiktaalik, for instance.
> And it separates Equus and Eohippus both equally from Hyracotherium --
> which is so close to Eohippus by every criterion except
> clade membership that it was LONG taken to be synonymous with Eohippus!

Exactly. That's a virtue of cladistic classification: that it doesn't
attempt to combine to incompatible criteria. Paraphyletic groups also
separate some similar taxa; you just don't think about those. Why?

>> Your argument is that it
>> unites "closely related" species. And yet it arbitrarily unites some
>> species and arbitrarily separates others. What's the point of that?
>
> The point is easily seen in Perissodactyla. Even if the Linnean
> system DID separate Eohippus and Hyracotherium from the rest of
> Equioidea, one could see that the rest is a family contiguous
> with the family "Eohippidae" and therefore the members of the
> two families together would only amount to a superfamily.

> The latter family would probably include all of Palaeotheridae
> and Hyrachius and some very primitive tapirs, but it's a nice
> compact family for all that. And it would be contiguous with
> the rhinoceros and tapir families, and so the whole kit and
> caboodle would be a superfamily.

That was highly unclear. I'm not clear what "contiguous" and "compact"
mean, exactly. So the point isn't as easily seen as you suppose. If I
have any idea what you mean by "contiguous", wouldn't monophyletic
groups also be contiguous?

And you're still drawing arbitrary lines that separate as many similar
species as they join. What's the justification for preferring to unite
the ones you unite and separate the ones you separate?

> If the Linnean system were allowed to evolve naturally,
> with its researchers not shut out of governmental grant money
> and out of positions at prestigious universities, the system
> would evolve more and more towards a system like a giant
> jigsaw puzzle with each new paleontological discovery.

Better dial down the rant. There is no conspiracy to shut out these
hypothetical "Linnean researchers" from anything.

> Contiguous sets of pieces could be the subject
> of essays on what the animals in each set have in common, and
> how one might identify an animal as belonging in one set or
> the other. Just as is the case with un-named, unranked clades.

> Does you wife like jigsaw puzzles? Maybe she could explain
> to you the merits of having a system like that, if the answer is Yes.
> Or if she likes quilts, that could be helpful too.

I would prefer if you would explain the merits to me. "Could be the
subject of essays" is not that great a recommendation.

>>>> Any classification that
>>>> splits the tree at any point must divide close relatives. It's a
>>>> physical impossibility to do otherwise. Thus the horizontal
>>>> classification doesn't have the advantage you suppose.
>>>
>>> I never supposed any such thing.
>>
>> Then I don't understand why you brought up horizontal classification or
>> what you think its advantage is.
>
> The advantages are the contributions they make to our understanding.
> I wish you would stop assuming that I think horizontal classifications
> are superior to vertical ones. I never did.

What contributions do they make to our understanding?

> And now, maybe you can see why I objected to the wording of
>
> 1. Can paraphyletic groups be more useful in classification
> than strict adherence to monophyly?
>
> It seems my initial answer still hasn't sunk in:
>
> Poorly worded. Ever since 2002 all I have ever argued for was for
> cladophiles like you not to ban paraphyletic groups, but to admit
> them side by side with monophyletic ones, because they also
> contribute to our understanding of evolution.

When you say "side by side" do you refer to a single classification in
which some groups are paraphyletic and others are not, or do you refer
to parallel classifications, one of which has entirely monophyletic
groups and the other of which has many paraphyletic groups? I dislike
either, but the latter is worse.

>> Why did you bring it up, and what do
>> you think its advantage is?
>
> I hope all the above helps. If it doesn't, please don't come up
> with condescending retorts like "Please stop hinting and say
> clearly what you mean." Try to figure out WHAT it is that you
> find unclear.

It didn't help. I don't think you actually addressed my argument or gave
any sensible reasons to designate any paraphyletic groups.

>> To use Romer's tree, suppose that within Family B, say at the first x
>> above B', we place another fossil, B''. B'', by the definition of
>> "closest relative" you prefer, should be classified along with B',
>> right?
>
> I don't do windows, and I don't do "closest relative." I do
> use "close relative" in various senses. Have you still not
> figured out that "members of the same Family" is Romer's
> *ad hoc* definition of "closely related" in Fig 1.?

No, I haven't, and I don't think it's true. I think he puts them in the
same family because he considers them closely related, which is just
backwards from your idea. And I don't see why you harp on a distinction
between "closest relative" and "close relative". My objection works as
well with either term, and you didn't address my point at all.

> All things are relative. You are far from me when the issue
> is walking from my place to yours. You are close to me
> when we are talking about astronomical units.

Not clear why that's relevant.

[Oxyaena]

True, which is why I said minor tweaks should be added to cladistics.
Your mileage does indeed vary from mine, I don't think crown group
definitions, while valid, are not always necessary and sometimes
unnecessarily exclude closely related sister taxa to the crown group
that share most if not all of the characteristics that characterize the
crown group.

Sometimes using a crown group justification can be justified, like the
crown group of Eutheria being Placentalia, but other times I don't think
it is, and adds confusion when there shouldn't be any. Take the
exclusion of Temnospondyli from Tetrapoda, when Tetrapoda was redefined
as the crown group consisting of the common ancestor of lissamphibians
and amniotes, and yet there is some debate over the origins of
lissamphibians, including the notion that the origins of Lissamphibia
lie inside Temnospondyli, while others say it lies inside Lepospondyli,
the point being that crown group definitions don't always take all the
factors into consideration.

[Oxyaena]

See below. There's no disagreement here. What I mean by "similarities"
is the number of shared genes between two clades.

[John Harshman]

That isn't what "similarities" means, and you are still talking about
mere similarity, not synapomorphy, unless you think that sharing of
genes can't be plesiomorphic.

[Peter Nyikos]

It's very relevant to the personal comment of yours immediately preceding
it, which it refutes.

> It's problematic for the acceptance of paraphyletic groups,

I don't see where it would cause any problem for cladists, since
the doctrinaire ones would ignore the paraphyletic groups anyway.

As for the more broad-minded ones, and all traditional taxonomists,
I believe the advantages more than outweigh the disadvantages,
once my "jigsaw puzzle" comments are taken into account.

> whether or not you think clades are fine too.
>
> > What YOU don't seem to see is that the cladistic system also
> > separates taxa from each other in the same way, taxa that
> > are closely related by Romer's usage.
>
> Of course it does. The cladistic system doesn't attempt not to separate
> similar-looking taxa. Similarity is not what cladistic classification is
> about.

And it isn't what the traditional classification has been about
for about the last century and a half.

> It attempts to recognize only cladistic relationships.

Nice to see you finally modify the word "relationships." It'll
make for a lot less talking past each other.


<snip straw man>

>
> > It separates the cow
> > and Elginerpeton both equally from Tiktaalik, for instance.
> > And it separates Equus and Eohippus both equally from Hyracotherium --
> > which is so close to Eohippus by every criterion except
> > clade membership that it was LONG taken to be synonymous with Eohippus!
>
> Exactly. That's a virtue of cladistic classification: that it doesn't
> attempt to combine to incompatible criteria. Paraphyletic groups also
> separate some similar taxa; you just don't think about those. Why?

You are pushing the envelope of our agreement with this false assumption
followed immediately by question-begging use of "Why?". The falsehood
of this one should have been suspected when you got to my talk
about contiguous families, which follows immediately below.

> >> Your argument is that it
> >> unites "closely related" species. And yet it arbitrarily unites some
> >> species and arbitrarily separates others. What's the point of that?
> >
> > The point is easily seen in Perissodactyla. Even if the Linnean
> > system DID separate Eohippus and Hyracotherium from the rest of
> > Equioidea, one could see that the rest is a family contiguous
> > with the family "Eohippidae" and therefore the members of the
> > two families together would only amount to a superfamily.
>
> > The latter family would probably include all of Palaeotheridae
> > and Hyrachius and some very primitive tapirs, but it's a nice
> > compact family for all that. And it would be contiguous with
> > the rhinoceros and tapir families, and so the whole kit and
> > caboodle would be a superfamily.
>
> That was highly unclear.

No, it wasn't. Any mathematician would know what I mean by the
two terms you are having trouble with below.

> I'm not clear what "contiguous" and "compact"
> mean, exactly. So the point isn't as easily seen as you suppose. If I
> have any idea what you mean by "contiguous", wouldn't monophyletic
> groups also be contiguous?

Didn't you try to look up the word in a good dictionary? Your question
reminds me of "the sound of one hand clapping."

"contiguous" is a relationship between two or more things. In many
concepts it refers to immediate adjacency. Here it refers to two
hypothetical families with some genera in one family C separated
from some genera in a family A whose members are descended from
some member of C and separated by a very small evolutionary distance,
like Eohippus and Epihippus, or Epihippus and Mesohippus, depending
on where the line is drawn.

> And you're still drawing arbitrary lines that separate as many similar
> species as they join.

Like almost any lines that one draws in real life. Are you being
carried away by the negative connotations of the word "arbitrary"?

> What's the justification for preferring to unite
> the ones you unite and separate the ones you separate?

No justification is needed where competent biologists are concerned;
it was not needed by Romer or Carroll. Try to find
books by cladists that compare to either of those two classics
in their scope. The closest I've come is Benton, but he is to
Carroll as Colbert was to Romer.

> > If the Linnean system were allowed to evolve naturally,
> > with its researchers not shut out of governmental grant money
> > and out of positions at prestigious universities, the system
> > would evolve more and more towards a system like a giant
> > jigsaw puzzle with each new paleontological discovery.
>
> Better dial down the rant. There is no conspiracy to shut out these
> hypothetical "Linnean researchers" from anything.

The word "conspiracy" is where the rant really begins. Government
grants for research are primarily based on how much additional
research the research, if successful, would generate. There simply
aren't enough traditional systematists around to justify grants
on that basis.

And you seriously underestimate the power of rationalization
that any cladistic systematist, fresh from the victory
in "the cladist wars" can hardly resist. Just look at the
way Obama used the words "We won" to stifle criticism.

Such a person could hardly have resisted the temptation to brand
work on a traditional classification as "too specialized." That is
the stock formula used by every prestigious mathematical journal
for rejection of any paper, no matter how un-specialized it is
in reality.

> > Contiguous sets of pieces could be the subject
> > of essays on what the animals in each set have in common, and
> > how one might identify an animal as belonging in one set or
> > the other. Just as is the case with un-named, unranked clades.
>
> > Does you wife like jigsaw puzzles? Maybe she could explain
> > to you the merits of having a system like that, if the answer is Yes.
> > Or if she likes quilts, that could be helpful too.
>
> I would prefer if you would explain the merits to me. "Could be the
> subject of essays" is not that great a recommendation.

Let's look at it this way. Traditional taxonomy is really like
many different jigsaw puzzle with huge differences in the number
of pieces. For middle school, a puzzle with the classes of vertebrates
would be enough -- let them get well acquainted with the
three classes of "fishes", and with the four classes of tetrapods.
For high school, a puzzle with the main subclasses and
infraclasses and superorders, including of course Dinosauria,
with the "well known fact" that birds are descended from dinosaurs.
For undergraduates, the puzzle includes most orders, especially
of mammals and birds. Heck, Peterson's Guides of birds still breaks
them down into orders and families, with no regard as to whether
any of them are paraphyletic.

Really big jigsaw puzzles are detailed at the end of Romer's
and Carroll's books. And those go down only to families.
A paleontologist could spend a lifetime getting a good picture
of what each subfamily of Chordata is/was like. But if he
knows how the pieces fit together, he can move from one piece
to adjacent pieces without having to start from scratch.

There is this wonderful thing known as learning for the love
of knowledge. You get all starry-eyed about it whenever I get
to talking about the financial advantages to countless
paleontologists to have birds descended from dinosaurs rather
than from crocodylians. But you lose sight of it whenever
you claim not to see any advantage to having ancestor candidates,
or paraphyletic taxa like "Rhipidistia," for example.

> >>>> Any classification that
> >>>> splits the tree at any point must divide close relatives. It's a
> >>>> physical impossibility to do otherwise. Thus the horizontal
> >>>> classification doesn't have the advantage you suppose.
> >>>
> >>> I never supposed any such thing.
> >>
> >> Then I don't understand why you brought up horizontal classification or
> >> what you think its advantage is.
> >
> > The advantages are the contributions they make to our understanding.
> > I wish you would stop assuming that I think horizontal classifications
> > are superior to vertical ones. I never did.
>
> What contributions do they make to our understanding?

See above for groups. You seem to think lists of apomorphies at each node
in the tree of life is conducive to better grasp of the hypothetical
LCA at each node than an ancestor candidate whose thousands of
characters can be studied at leisure. Do you want to replace
scientists with computers?


Remainder deleted, to be replied to next week.


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

[John Harshman]

This is all a pointless semantic quibble. Let's not.

>> It's problematic for the acceptance of paraphyletic groups,
>
> I don't see where it would cause any problem for cladists, since
> the doctrinaire ones would ignore the paraphyletic groups anyway.
>
> As for the more broad-minded ones, and all traditional taxonomists,
> I believe the advantages more than outweigh the disadvantages,
> once my "jigsaw puzzle" comments are taken into account.

Your "jigsaw puzzle" comments are of obscure meaning, so it would be
hard for anyone to take tham into account. The "doctrinaire" bit is an
actual ad hominem argument (as opposed to what is usually referred to by
that name around here, incorrectly).

What you need to do is present an argument in opposition to mine.

>> whether or not you think clades are fine too.
>>
>>> What YOU don't seem to see is that the cladistic system also
>>> separates taxa from each other in the same way, taxa that
>>> are closely related by Romer's usage.
>>
>> Of course it does. The cladistic system doesn't attempt not to separate
>> similar-looking taxa. Similarity is not what cladistic classification is
>> about.
>
> And it isn't what the traditional classification has been about
> for about the last century and a half.

Yes, it is. Have you ever actually read any of the systematics
literature? Mayr's discussions of the matter are fairly illuminating.
Again, "evolutionary" classification is an attempt to reconcile
cladistic relationships and morphological similarity, with the result
that neither is dependably represented.

>> It attempts to recognize only cladistic relationships.
>
> Nice to see you finally modify the word "relationships." It'll
> make for a lot less talking past each other.

This is hardly the first time I've used the term.

>>> It separates the cow
>>> and Elginerpeton both equally from Tiktaalik, for instance.
>>> And it separates Equus and Eohippus both equally from Hyracotherium --
>>> which is so close to Eohippus by every criterion except
>>> clade membership that it was LONG taken to be synonymous with Eohippus!
>>
>> Exactly. That's a virtue of cladistic classification: that it doesn't
>> attempt to combine to incompatible criteria. Paraphyletic groups also
>> separate some similar taxa; you just don't think about those. Why?
>
> You are pushing the envelope of our agreement with this false assumption
> followed immediately by question-begging use of "Why?". The falsehood
> of this one should have been suspected when you got to my talk
> about contiguous families, which follows immediately below.

Please, rather than taking offense, make some kind of response to the
substance of what I say. Why is it false?

>>>> Your argument is that it
>>>> unites "closely related" species. And yet it arbitrarily unites some
>>>> species and arbitrarily separates others. What's the point of that?
>>>
>>> The point is easily seen in Perissodactyla. Even if the Linnean
>>> system DID separate Eohippus and Hyracotherium from the rest of
>>> Equioidea, one could see that the rest is a family contiguous
>>> with the family "Eohippidae" and therefore the members of the
>>> two families together would only amount to a superfamily.
>>
>>> The latter family would probably include all of Palaeotheridae
>>> and Hyrachius and some very primitive tapirs, but it's a nice
>>> compact family for all that. And it would be contiguous with
>>> the rhinoceros and tapir families, and so the whole kit and
>>> caboodle would be a superfamily.
>>
>> That was highly unclear.
>
> No, it wasn't. Any mathematician would know what I mean by the
> two terms you are having trouble with below.

I'm not a mathematician. Clarity is the experience of the reader and the
responsibility of the writer. Just saying "no, it wasn't" helps nobody.

>> I'm not clear what "contiguous" and "compact"
>> mean, exactly. So the point isn't as easily seen as you suppose. If I
>> have any idea what you mean by "contiguous", wouldn't monophyletic
>> groups also be contiguous?
>
> Didn't you try to look up the word in a good dictionary? Your question
> reminds me of "the sound of one hand clapping."

I grow weary of the constant passive-aggressive accusations.

> "contiguous" is a relationship between two or more things. In many
> concepts it refers to immediate adjacency. Here it refers to two
> hypothetical families with some genera in one family C separated
> from some genera in a family A whose members are descended from
> some member of C and separated by a very small evolutionary distance,
> like Eohippus and Epihippus, or Epihippus and Mesohippus, depending
> on where the line is drawn.

That is no more clear than your previous attempt. Less so, in fact,
since you now disown the dictionary definition. So in order to be
contiguous, one taxon must be paraphyletic to the other? That's a highly
counterintuitive definition.

What is the advantage of one "contiguous" pair over another, and of a
contiguous pair over a mutually monophyletic pair?

>> And you're still drawing arbitrary lines that separate as many similar
>> species as they join.
>
> Like almost any lines that one draws in real life. Are you being
> carried away by the negative connotations of the word "arbitrary"?

The point is that there is no advantage over cladistic classification,
as your paraphyletic groups separate similar species just as much as
strictly monophyletic ones.

>> What's the justification for preferring to unite
>> the ones you unite and separate the ones you separate?
>
> No justification is needed where competent biologists are concerned;
> it was not needed by Romer or Carroll. Try to find
> books by cladists that compare to either of those two classics
> in their scope. The closest I've come is Benton, but he is to
> Carroll as Colbert was to Romer.

I'm sorry, but appeal to authority is not a proper argument. Try again.

>>> If the Linnean system were allowed to evolve naturally,
>>> with its researchers not shut out of governmental grant money
>>> and out of positions at prestigious universities, the system
>>> would evolve more and more towards a system like a giant
>>> jigsaw puzzle with each new paleontological discovery.
>>
>> Better dial down the rant. There is no conspiracy to shut out these
>> hypothetical "Linnean researchers" from anything.
>
> The word "conspiracy" is where the rant really begins. Government
> grants for research are primarily based on how much additional
> research the research, if successful, would generate. There simply
> aren't enough traditional systematists around to justify grants
> on that basis.

Do you have any actual evidence for the claim that granting bodies think
about this sort of thing?

> And you seriously underestimate the power of rationalization
> that any cladistic systematist, fresh from the victory
> in "the cladist wars" can hardly resist.

Do you have any actual knowledge of such a thing? [gratuitous reference
to third party snipped]

> Such a person could hardly have resisted the temptation to brand
> work on a traditional classification as "too specialized." That is
> the stock formula used by every prestigious mathematical journal
> for rejection of any paper, no matter how un-specialized it is
> in reality.

Again, do you have any actual knowledge of anything like this being done
by a systematist, or are you just reasoning by analogy with mathematics?
I don't find that a valid argument.

>>> Contiguous sets of pieces could be the subject
>>> of essays on what the animals in each set have in common, and
>>> how one might identify an animal as belonging in one set or
>>> the other. Just as is the case with un-named, unranked clades.
>>
>>> Does you wife like jigsaw puzzles? Maybe she could explain
>>> to you the merits of having a system like that, if the answer is Yes.
>>> Or if she likes quilts, that could be helpful too.
>>
>> I would prefer if you would explain the merits to me. "Could be the
>> subject of essays" is not that great a recommendation.
>
> Let's look at it this way. Traditional taxonomy is really like
> many different jigsaw puzzle with huge differences in the number
> of pieces. For middle school, a puzzle with the classes of vertebrates
> would be enough -- let them get well acquainted with the
> three classes of "fishes", and with the four classes of tetrapods.
> For high school, a puzzle with the main subclasses and
> infraclasses and superorders, including of course Dinosauria,
> with the "well known fact" that birds are descended from dinosaurs.
> For undergraduates, the puzzle includes most orders, especially
> of mammals and birds.

This whole "puzzle" metaphor serves no useful purpose. If you're saying
that paraphyletic groups are fine for children but should be abandoned
by adults, that might be defensible. But I dont' think you actually mean
that.

> Heck, Peterson's Guides of birds still breaks
> them down into orders and families, with no regard as to whether
> any of them are paraphyletic.

Peterson is quite an old guide. More recent guides have moved species
around to make the taxa monophyletic.

> Really big jigsaw puzzles are detailed at the end of Romer's
> and Carroll's books. And those go down only to families.
> A paleontologist could spend a lifetime getting a good picture
> of what each subfamily of Chordata is/was like. But if he
> knows how the pieces fit together, he can move from one piece
> to adjacent pieces without having to start from scratch.

Again, the puzzle metaphor is opaque here. I see no argument for the
value of paraphyletic taxa. Perhaps if you made it directly, abandoning
the opaque metaphor?

> There is this wonderful thing known as learning for the love
> of knowledge. You get all starry-eyed about it whenever I get
> to talking about the financial advantages to countless
> paleontologists to have birds descended from dinosaurs rather
> than from crocodylians. But you lose sight of it whenever
> you claim not to see any advantage to having ancestor candidates,
> or paraphyletic taxa like "Rhipidistia," for example.

That isn't learning for the love of knowledge. It's learning for the
love of illusion. No scientific purpose is served, and even the wonder
of it is just what you're used to. I find greater wonder in the actual
clades within clades, which have the virtue of being real entities.

It might help if you would actually explain what the advantages are. So
far the advantage seems to be that it makes things easier for you,
personally, to visualize. I don't find that a good argument.

>>>>>> Any classification that
>>>>>> splits the tree at any point must divide close relatives. It's a
>>>>>> physical impossibility to do otherwise. Thus the horizontal
>>>>>> classification doesn't have the advantage you suppose.
>>>>>
>>>>> I never supposed any such thing.
>>>>
>>>> Then I don't understand why you brought up horizontal classification or
>>>> what you think its advantage is.
>>>
>>> The advantages are the contributions they make to our understanding.
>>> I wish you would stop assuming that I think horizontal classifications
>>> are superior to vertical ones. I never did.
>>
>> What contributions do they make to our understanding?
>
> See above for groups.

I saw nothing other than an unclear allusion to puzzle pieces. This is
not working for you. Please try again without the metaphor.

> You seem to think lists of apomorphies at each node
> in the tree of life is conducive to better grasp of the hypothetical
> LCA at each node than an ancestor candidate whose thousands of
> characters can be studied at leisure. Do you want to replace
> scientists with computers?

No. But yes, one can better grasp the ancestor by reconstructing it on a
densely populated tree than by declaring some convenient fossil to be an
ancestor candidate.

Science does advance, and advances in scientific methodology are a
factor in that advance. I think you're just clinging emotionally to the
way it used to be because it's what you learned when you were young.
Actual science has moved on. You can call modern systematists a bunch of
blind fools if you like, but that's not an argument either.