Turtle genome sequence and analysis

[Ron O]

Another interesting genome has been published. It comes from the same
lineage as crocs, dinos and birds.

http://genomebiology.com/2013/14/3/R28/abstract

The article is open access, but I wouldn't print it out. In
prepublication form it is over 70 pages.

This turtle's genome appears to evolve more slowly than mammal
genomes. They claim a rate 1/3 of that of humans. Also of interest
to this group is that they looked at the genes associated with teeth
(turtles lost their teeth) and found the same genes degenerating in
the genome as are found in birds. More evidence of common descent and
inheriting a genome from an ancestor with teeth. Losing teeth is a
tricky proposition. You have to maintain the cranial structure of the
ancestral type, but get rid of the teeth. So you need to keep some
aspects of developing teeth, while changing others.

These kinds of finds will keep coming. The 10,000 animal genome
project has turned into 100,000 so over the next few years there is
going to be so much genomic sequence available that we could probably
take a century analyzing it.

Some researchers are already doing population scale genome analysis,
not just individual genomes of individual species. The 1,000 human
genome project turned into the 10,000 human genome project and they
have pretty much covered the first thousand and are working on the
10,000.

Ron Okimoto

[pnyikos]

On Mar 29, 7:04锟絘m, Ron O <rokim...@cox.net> wrote:
> Another interesting genome has been published. 锟絀t comes from the same

> lineage as crocs, dinos and birds.

This has been disputed by Gauthier and others, based on fossil
evidence. They even dispute the claim that turtles are secondarily,
rather than primarily, anapsid. If they are right, turtles are the
outliers of extant Sauropsida.

> http://genomebiology.com/2013/14/3/R28/abstract

I looked at the available PDF of the whole provisional article, and a
word search turns up no instances of the word "Sphenodon." [I even
searched for the letter string "Rhync".]

This is a serious omission. Fossil evidence has generally been
interpreted as having Sphenodon as the sister group of archosaurs
among living taxa.

This seems to be a recurring theme -- fossil evidence leading to
opposite conclusions than genomic evidence. We saw it in the case
where genomic evidence leads researchers to place the LCA of living
placental (as opposed to marsupial, etc) mammals at ca. 105 mya, while
fossil evidence was interpreted by them to place it past the K-T
extinction event.

For more details, see:

http://groups.google.com/group/sci.bio.paleontology/msg/d0ec8fc6d5deed91

> The article is open access, but I wouldn't print it out. 锟絀n

> prepublication form it is over 70 pages.
>
> This turtle's genome appears to evolve more slowly than mammal

> genomes. 锟絋hey claim a rate 1/3 of that of humans.

I wonder how they established this, and what the evidence would show
as the rate of evolution of Sphenodon. Osteologically it is a "living
fossil," hardly changed since Jurassic times.


>锟紸lso of interest

> to this group is that they looked at the genes associated with teeth
> (turtles lost their teeth) and found the same genes degenerating in

> the genome as are found in birds. 锟組ore evidence of common descent and

> inheriting a genome from an ancestor with teeth.

If those same genes are found in Sphenodon, that could be significant.

> 锟絃osing teeth is a
> tricky proposition. 锟結ou have to maintain the cranial structure of the

> ancestral type, but get rid of the teeth.

I can see that where *gaining* teeth is concerned, but why *losing*
teeth?

> So you need to keep some
> aspects of developing teeth, while changing others.

I still don't get it.


> These kinds of finds will keep coming. 锟絋he 10,000 animal genome

> project has turned into 100,000 so over the next few years there is
> going to be so much genomic sequence available that we could probably
> take a century analyzing it.
>
> Some researchers are already doing population scale genome analysis,

> not just individual genomes of individual species. 锟絋he 1,000 human

> genome project turned into the 10,000 human genome project and they
> have pretty much covered the first thousand and are working on the
> 10,000.

I've read in one place, though, that the whole human genome has not
actually been sequenced, because e.g. some junk DNA remains
unsequenced. Do you know anything about this?

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

[John Harshman]

On 3/29/13 9:26 AM, pnyikos wrote:
> On Mar 29, 7:04 am, Ron O<rokim...@cox.net> wrote:
>> Another interesting genome has been published. It comes from the same

>> lineage as crocs, dinos and birds.
>
> This has been disputed by Gauthier and others, based on fossil
> evidence. They even dispute the claim that turtles are secondarily,
> rather than primarily, anapsid. If they are right, turtles are the
> outliers of extant Sauropsida.

If. The molecular data have been getting more and more conclusive in the
past few years. Turtles are either archosaurs of the living sister group
of archosaurs.

There is of course some morphological evidence that they are at least
diapsids, mostly advanced by Olivier Rieppel and colleagues.

>> http://genomebiology.com/2013/14/3/R28/abstract
>
> I looked at the available PDF of the whole provisional article, and a
> word search turns up no instances of the word "Sphenodon." [I even
> searched for the letter string "Rhync".]
>
> This is a serious omission. Fossil evidence has generally been
> interpreted as having Sphenodon as the sister group of archosaurs
> among living taxa.

Are you sure? Usually it's interpreted as the sister of squamates.

> This seems to be a recurring theme -- fossil evidence leading to
> opposite conclusions than genomic evidence. We saw it in the case
> where genomic evidence leads researchers to place the LCA of living
> placental (as opposed to marsupial, etc) mammals at ca. 105 mya, while
> fossil evidence was interpreted by them to place it past the K-T
> extinction event.

It's a recurring theme only because you (and the world generally) take
note of the times it happens but not of the much more frequent times it
doesn't. Man bites dog.

> For more details, see:
>
> http://groups.google.com/group/sci.bio.paleontology/msg/d0ec8fc6d5deed91
>

>> The article is open access, but I wouldn't print it out. In

>> prepublication form it is over 70 pages.
>>
>> This turtle's genome appears to evolve more slowly than mammal

>> genomes. They claim a rate 1/3 of that of humans.

>
> I wonder how they established this, and what the evidence would show
> as the rate of evolution of Sphenodon. Osteologically it is a "living
> fossil," hardly changed since Jurassic times.

There is no apparent correlation, based on all sorts of data in all
sorts of taxa, between morphological and molecular evolutionary rates.
"How they established this" is presumably either by comparison of both
with outgroups ("relative rate test") or by using time-calibrated
phylogenies.

>> Also of interest

>> to this group is that they looked at the genes associated with teeth
>> (turtles lost their teeth) and found the same genes degenerating in

>> the genome as are found in birds. More evidence of common descent and

>> inheriting a genome from an ancestor with teeth.
>
> If those same genes are found in Sphenodon, that could be significant.

Surely that conclusion isn't controversial. Regardless of relationships,
both bird and turtle ancestors had teeth.

>> Losing teeth is a
>> tricky proposition. You have to maintain the cranial structure of the

>> ancestral type, but get rid of the teeth.
>
> I can see that where *gaining* teeth is concerned, but why *losing*
> teeth?

Not clear to me either. The presumption here would be that developing
teeth are crucial in the development of other parts of the skull. That
seems an odd proposition.

>> So you need to keep some
>> aspects of developing teeth, while changing others.
>
> I still don't get it.
>
>

>> These kinds of finds will keep coming. The 10,000 animal genome

>> project has turned into 100,000 so over the next few years there is
>> going to be so much genomic sequence available that we could probably
>> take a century analyzing it.
>>
>> Some researchers are already doing population scale genome analysis,

>> not just individual genomes of individual species. The 1,000 human

>> genome project turned into the 10,000 human genome project and they
>> have pretty much covered the first thousand and are working on the
>> 10,000.
>
> I've read in one place, though, that the whole human genome has not
> actually been sequenced, because e.g. some junk DNA remains
> unsequenced. Do you know anything about this?

A few bits are hard to sequence, like very GC-rich segments. What's more
important is that some are hard to assemble once you've sequences them,
like highly repetitive DNA, which is also most likely to differ
significantly among individuals.

[Ron O]

On Mar 29, 11:26�am, pnyikos <nyik...@bellsouth.net> wrote:
> On Mar 29, 7:04�am, Ron O <rokim...@cox.net> wrote:

Face it Nyikos about the only post that I want to see from you is your
third self inflicted knockdown post so that you will just leave me
alone. The knockdown never appeared in February like you claimed that
it would or in January like you claimed it would or soon after your
second stupidity last October.

What makes you think that I am at all interested in what you have to
post after your last assoholic episode? What a loser.

Ron Okimoto

[pnyikos]

On Mar 29, 12:47 pm, John Harshman <jharsh...@pacbell.net> wrote:
> On 3/29/13 9:26 AM, pnyikos wrote:
>
> > On Mar 29, 7:04 am, Ron O<rokim...@cox.net>  wrote:
> >> Another interesting genome has been published.  It comes from the same
> >> lineage as crocs, dinos and birds.
>
> > This has been disputed by Gauthier and others, based on fossil
> > evidence.  They even dispute the claim that turtles are secondarily,
> > rather than primarily, anapsid.  If they are right, turtles are the
> > outliers of extant Sauropsida.
>
> If. The molecular data have been getting more and more conclusive in the
> past few years. Turtles are either archosaurs of the living sister group
> of archosaurs.
>
> There is of course some morphological evidence that they are at least
> diapsids, mostly advanced by Olivier Rieppel and colleagues.

Not here, unless one of the co-authors here is a colleague:

> >>http://genomebiology.com/2013/14/3/R28/abstract

Are you referring to the papers listed in the following passage?

"The position of turtles (Testudines) is uncertain; some authors place
them approximately in the position shown above (Laurin & Reisz, 1995;
Lee, 1993, 1995, 2001; Frost et al., 2006; Werneburg & Sánchez-
Villagra, 2009; Lyson et al. 2010), while others place them among
Diapsida (deBraga & Rieppel, 1996, 1997; Rieppel & Reisz, 1999; Hedges
& Poling, 1999; Mannen & Li, 1999; Hugall et al., 2007; Li et al.,
2008)."
-- caption to phylogenetic tree of Amniota in
http://tolweb.org/Amniota/14990

The tree shows turtles (Testudines) in Anapsida.

Laurin and Gauthier, who did the site, see your Rieppel et.al. ...1999
and raise it to 2010.

Later down in the page they write:

"At least two total evidence analyses (in which molecular and
morphological data are combined) suggest that turtles are not diapsids
(Lee, 2001; Frost et al., 2006). In both, the molecular characters are
much more numerous than the morphological ones, which implies
significant support for the placement of turtles outside diapsids in
these molecular datasets."

I wonder who is cherry-picking this time, you or they.

> > I looked at the available PDF of the whole provisional article, and a
> > word search turns up no instances of the word "Sphenodon."  [I even
> > searched for the letter string "Rhync".]
>
> > This is a serious omission.  Fossil evidence has generally been
> > interpreted as having Sphenodon as the sister group of archosaurs
> > among living taxa.
>
> Are you sure? Usually it's interpreted as the sister of squamates.

You are correct, I remembered those old "bubble diagrams"
incorrectly.

However, if Sphenodon evolved much more slowly (molecularlty speaking)
than either birds, crocs, or squamates, then a traditional systematist
would say it is much more closely related to the LCA of the whole
diapsid clade than any of them.

Then a race would be on to see whether tortoises or Sphenodon are
more closely related to the LCA.

This is one race where the slower is the winner. No hares need
apply.

Continued in next post.

[pnyikos]

On Mar 29, 12:47�pm, John Harshman <jharsh...@pacbell.net> wrote:

> On 3/29/13 9:26 AM, pnyikos wrote:
>
> > On Mar 29, 7:04 am, Ron O<rokim...@cox.net> �wrote:

> > This seems to be a recurring theme -- fossil evidence leading to
> > opposite conclusions than genomic evidence. �We saw it in the case
> > where genomic evidence leads researchers to place the LCA of living
> > placental (as opposed to marsupial, etc) mammals at ca. 105 mya, while
> > fossil evidence was interpreted by them to place it past the K-T
> > extinction event.
>
> It's a recurring theme only because you (and the world generally) take
> note of the times it happens but not of the much more frequent times it
> doesn't.

Either that, or there are many other times having to do with closely
related taxa, and so they escape notice. [For cladophiles like you, I
should write "molecularly and morphologically similar" rather than
"closely related" so as to make it intelligible to you.]

> Man bites dog.

Or maybe "cats bite hundreds of dogs, but it is only when man gets
into the act that news reporters take notice."

> > For more details, see:
>
> >http://groups.google.com/group/sci.bio.paleontology/msg/d0ec8fc6d5deed91
>
> >> The article is open access, but I wouldn't print it out. �In
> >> prepublication form it is over 70 pages.
>
> >> This turtle's genome appears to evolve more slowly than mammal
> >> genomes. �They claim a rate 1/3 of that of humans.
>
> > I wonder how they established this, and what the evidence would show
> > as the rate of evolution of Sphenodon. Osteologically it is a "living
> > fossil," hardly changed since Jurassic times.
>
> There is no apparent correlation, based on all sorts of data in all
> sorts of taxa, between morphological and molecular evolutionary rates.

However, I am still curious to know what the situation is with
Sphenodon, as suggested in my first reply.

> "How they established this" is presumably either by comparison of both
> with outgroups ("relative rate test") or by using time-calibrated
> phylogenies.

The details would be nice to know.

> >> � Also of interest

> >> to this group is that they looked at the genes associated with teeth
> >> (turtles lost their teeth) and found the same genes degenerating in
> >> the genome as are found in birds. �More evidence of common descent and
> >> inheriting a genome from an ancestor with teeth.

Yet another of millions of little nails in the coffin of creationism.

> > If those same genes are found in Sphenodon, that could be significant.
>
> Surely that conclusion isn't controversial. Regardless of relationships,
> both bird and turtle ancestors had teeth.

Well, duh. I was interested in how much light the same genes in
Sphenodon shed on what the LCA of extant Sauropsida was like.

> >> � Losing teeth is a

> >> tricky proposition. �You have to maintain the cranial structure of the
> >> ancestral type, but get rid of the teeth.
>
> > I can see that where *gaining* teeth is concerned, but why *losing*
> > teeth?
>
> Not clear to me either. The presumption here would be that developing
> teeth are crucial in the development of other parts of the skull. That
> seems an odd proposition.

Ron O doesn't want to discuss this with me, but I was hoping he would
discuss it with you. But so far, it's no go.

Maybe if you replied to him directly...

Peter Nyikos

[pnyikos]

On Mar 29, 5:37 pm, Ron O <rokim...@cox.net> neglected to snip the
following attributions, but snipped all the text from the posts to
which they refer.

> On Mar 29, 11:26 am, pnyikos <nyik...@bellsouth.net> wrote:
>
> > On Mar 29, 7:04 am, Ron O <rokim...@cox.net> wrote:

By some people's standards [but not mine], Ron O replied to himself:

> Face it Nyikos about the only post that I want to see from you

would be off topic, and so nothing on the same topic is going to be
posted by me here.

Post your off-topic taunts on some thread where they are no more off-
topic than some of the surrounding posts.

[snip rest of off-topic taunt]

Note to others: if anyone besides Ron O thinks what I snipped is
worthy of being addressed, I'll address it on a more appropriate
thread. Otherwise I'm finished with it.

For the benefit of these hypothetical readers, the Ron O post to
which I am replying can be found here:

http://groups.google.com/group/talk.origins/msg/98b5a70fff8f9a50

Peter Nyikos

[Ron O]

On Apr 4, 2:26�pm, pnyikos <nyik...@bellsouth.net> wrote:
> On Mar 29, 5:37�pm, Ron O <rokim...@cox.net> neglected to snip the
> following attributions, but snipped all the text from the posts to
> which they refer.
>
> > On Mar 29, 11:26 am, pnyikos <nyik...@bellsouth.net> wrote:
>
> > > On Mar 29, 7:04 am, Ron O <rokim...@cox.net> wrote:
>
> By some people's �standards [but not mine], Ron O replied to himself:
>
> > Face it Nyikos about the only post that I want to see from you
>
> would be off topic, and so nothing on the same topic is going to be
> posted by me here.

How delusional can a person get? Nyikos is the king of posting stupid
junk to other posters in other threads, and he balks at what? Doing
what he claimed that he would do nearly a year and a half ago.

My post was so short that the only reason why Nyikos would snip any of
it out is to cowardly run away from reality again.

QUOTE:

Face it Nyikos about the only post that I want to see from you is your
third self inflicted knockdown post so that you will just leave me
alone. The knockdown never appeared in February like you claimed that
it would or in January like you claimed it would or soon after your
second stupidity last October.

What makes you think that I am at all interested in what you have to
post after your last assoholic episode? What a loser.

END QUOTE:

Really, after all the bull shit that Nyikos is guilty of over more
than 2 years he has to claim that he is unwilling to post something
that is off topic? Who changed the name of the thread and started a
totally off topic side thread and claimed it as his second knockdown?
That was Nyikos. The guy that just made up the stupid story that he
claimed was so funny in that side thread. You can't make this junk
up. Nyikos will always do himself one better in the bogousity
department.

>
> Post your off-topic taunts on some thread where they are no more off-
> topic than some of the surrounding posts.

You are the one that posted to me. What an asshole. Do I care about
your opinion on anything? No.

Now all you can do is run. How sad is that? Who has been claiming
that the hammer blows and knockdowns are coming for nearly a year and
a half? Who has been the pathetic liar and pretender in all that
time?

>
> [snip rest of off-topic taunt]
>
> Note to others: if anyone besides Ron O thinks what I snipped is
> worthy of being addressed, I'll address it on a more appropriate
> thread. Otherwise I'm finished with it.

Cowards lie and run. Nyikos is not just an asshole, but he is a
cowardly lying asshole. The sad thing is that Nyikos knows what he is
and has to run from reality. Who has been bleating and lying about me
to other posters? Who can't face reality and has to run and bleat to
everyone else?

>
> For the benefit of these hypothetical readers, �the Ron O post to
> which I am replying can be found here:
>
> http://groups.google.com/group/talk.origins/msg/98b5a70fff8f9a50
>
> Peter Nyikos

Nyikos, just deliver your third stupid knockdown and just run for
good. Why keep coming back to whine and bleat about bogus junk that
you did years ago? Just do what you bragged about doing over a year
ago and then don't darken my door again. I will, of course, have to
demonstrate what a whacked out loser you are when you do deliver the
non existent knockdown and punch yourself in the face again. So just
do it and then whine and bleat to your hearts content, just don't
bother posting to me unless you like being reminded what a low life
cowardly lying scum bag you are.

Really, instead of continuing to whine and bleat, just deliver your
third stupid knockdown and run away for good. How many times are you
going to say that you are going to deliver it and then end up lying?
Did it come soon in October? Did it come in January like you said
that it would? Did it come in February like you said that it would?
What kind of whining and bleating were you doing instead of delivering
your stupid knockdown for the last couple of months? Why shouldn't I
be ticked off? You are such a degenerate loser and all you do is keep
coming back with your stupid junk time and time again. Well just
deliver the stupid knockdown and quit like you said that you would.
Just think of it as one last lie that you have to tell. That should
help the pathological liar passed his yellow streak.

Nyikos can call this taunting, but he knows for a fact that it is all
true. So just deliver your third stupid knockdown and stop posting to
me like you said that you would over a year ago.

Ron Okimoto

[Burkhard]

Ok, that's it, and with some regret, as you on occasions post
interesting stuff, but your pathological obsession makes the noise
information ratio well below acceptable, not to mention lacking basic
civility in posting. Plonk

[Ron O]

I'm the one that has had enough. I still can't understand why anyone
would want to read junk that involves Nyikos. I stopped reading most
of the crap Nyikos posts 2 years ago.

Ron Okimoto

[Richard Norman]

On Thu, 4 Apr 2013 16:52:30 -0700 (PDT), Ron O <roki...@cox.net>
wrote:

If you stopped reading it then how come you respond so vociferously
and at such enormous length? Why do you think we tolerate your crap
about him any better than his rants? Why don't both of you just give
it a rest? Even one of you calling it quits would be an enormous
improvement. Nobody here would think the other would "win" just
because there is no response. On the contrary, we all would win by
not being buried in this trash.

That being said, this is an open news group and you can post whatever
you wish consonant with or contrary to my advice. Plonk.

[Ron O]

On Apr 4, 7:36�pm, Richard Norman <r_s_nor...@comcast.net> wrote:
> On Thu, 4 Apr 2013 16:52:30 -0700 (PDT), Ron O <rokim...@cox.net>

Why do you respond to any post?

If you read much of anything by Nyikos you likely know that most of
what he posts about me isn't to me. Hasn't been since he went on his
knockdown bull pucky nearly a year and a half ago. What has Nyikos
been doing with respect to me in that year and a half? I have no
control over what Nyikos posts to anyone else, but when he posts his
crap to me I don't mind letting him know what a lowlife scum bag he
is. It is the only thing that keeps him away for any length of time.
When he screws up really badly it will be months before he posts to me
again. That is all that I can hope for. What has he been doing since
October and his last stupid knockdown attempt? Basically only whining
and bleating and claiming that his third knockdown is coming. That is
all that I have had to put up with.

Do I want him to post to me? Obviously, not. I can't be more clear
on the subject, but if you have tried to talk sense to the dishonest
asshole you know what a lost cause it is. The only thing that I can
hope for is that he will one day deliver his last stupid knockdown and
run away for good. What else can I do? Do I follow him around the
internet posting stupid crap to him? No.

Anyone that wants to waste a lot of time can just check out the
facts. Weeks and months will go by when Nyikos doesn't post to me,
but you guys just see him whinning and bleating about me and think
that we are going at it. I'm not there. Between last July and
October there were 3 months where Nyikos did not post to me. No one
seems to have noticed because Nyikos carried on bleating and whining
even when he was running. I wasn't there. Nyikos was just blustering
while running from his stupid threats to deliver his knockdowns. It
was all Nyikos. Really, between Nyikos' first self inflicted
knockdown his second pathetic bout of punching himself in the face
(October to October) there was over half a year of extended periods of
time of over a month where I did not post to Nyikos because he did not
post to me. He was busy posting his crap to other posters. You guys
had to deal with Nyikos' bleating and whining. The only reason Nyikos
has posted more often to me since October is because he has to keep
claiming that his third knockdown is still coming after missing his
own deadlines. It became his monthly public service announcement. I
can't do anything about Nyikos' stupidity. I can only point out what
he is doing and demonstrate how wrong it is so that he will run and
leave me alone for a few weeks. He isn't stupid. He understands when
he has been a degenerate asshole. It is the only thing that shuts him
up until he decides to lie about something else.

Nyikos is the one that said that he was going to deliver his
knockdowns and then stop posting to me and that was over a year ago.
I never told Nyikos that I would not respond to his posts to me. I've
just told him that I had no problem demonstrating what a jerk he is.
If you have a solution to the Nyikos problem don't keep it a secret.
It isn't that it is becoming too stupid to be believable. It has been
that way for nearly a year and a half after Nyikos gave up on what we
were arguing about. Nyikos no longer contests that he was wrong. All
you see him doing for the last year and a half is lying about what he
did during the time that we were arguing over how wrong he was, and
threatening to lower the hammer and deliver his stupid knockdowns.

Plonk yourself. Ignorance is obviously bliss. I've had to live the
Nyikos stupidity.

Ron Okimoto

[jillery]

Since you say you believe both are equally to blame, I hope you are
plonking the both of them, else you are putting the blame entirely on
Ron O., the lie to your expressed complaint, and giving rockhead
exactly what he wants.

[John Harshman]

On 4/4/13 11:54 AM, pnyikos wrote:
> On Mar 29, 12:47 pm, John Harshman<jharsh...@pacbell.net> wrote:
>> On 3/29/13 9:26 AM, pnyikos wrote:
>>
>>> On Mar 29, 7:04 am, Ron O<rokim...@cox.net> wrote:
>>>> Another interesting genome has been published. It comes from the same
>>>> lineage as crocs, dinos and birds.
>>
>>> This has been disputed by Gauthier and others, based on fossil
>>> evidence. They even dispute the claim that turtles are secondarily,
>>> rather than primarily, anapsid. If they are right, turtles are the
>>> outliers of extant Sauropsida.
>>
>> If. The molecular data have been getting more and more conclusive in the
>> past few years. Turtles are either archosaurs of the living sister group
>> of archosaurs.
>>
>> There is of course some morphological evidence that they are at least
>> diapsids, mostly advanced by Olivier Rieppel and colleagues.
>
> Not here, unless one of the co-authors here is a colleague:
>
>>>> http://genomebiology.com/2013/14/3/R28/abstract
>
> Are you referring to the papers listed in the following passage?
>
> "The position of turtles (Testudines) is uncertain; some authors place

> them approximately in the position shown above (Laurin& Reisz, 1995;
> Lee, 1993, 1995, 2001; Frost et al., 2006; Werneburg& S�nchez-

> Villagra, 2009; Lyson et al. 2010), while others place them among

> Diapsida (deBraga& Rieppel, 1996, 1997; Rieppel& Reisz, 1999; Hedges
> & Poling, 1999; Mannen& Li, 1999; Hugall et al., 2007; Li et al.,

> 2008)."
> -- caption to phylogenetic tree of Amniota in
> http://tolweb.org/Amniota/14990

The ones by Rieppel are among the ones I was referring to.

> The tree shows turtles (Testudines) in Anapsida.

Since the various references conflict, they picked one over the others.

> Laurin and Gauthier, who did the site, see your Rieppel et.al. ...1999
> and raise it to 2010.
>
> Later down in the page they write:
>
> "At least two total evidence analyses (in which molecular and
> morphological data are combined) suggest that turtles are not diapsids
> (Lee, 2001; Frost et al., 2006). In both, the molecular characters are
> much more numerous than the morphological ones, which implies
> significant support for the placement of turtles outside diapsids in
> these molecular datasets."
>
> I wonder who is cherry-picking this time, you or they.

Neither. What does any of this have to do with what I said?

>>> I looked at the available PDF of the whole provisional article, and a
>>> word search turns up no instances of the word "Sphenodon." [I even
>>> searched for the letter string "Rhync".]
>>
>>> This is a serious omission. Fossil evidence has generally been
>>> interpreted as having Sphenodon as the sister group of archosaurs
>>> among living taxa.
>>
>> Are you sure? Usually it's interpreted as the sister of squamates.
>
> You are correct, I remembered those old "bubble diagrams"
> incorrectly.
>
> However, if Sphenodon evolved much more slowly (molecularlty speaking)
> than either birds, crocs, or squamates, then a traditional systematist
> would say it is much more closely related to the LCA of the whole
> diapsid clade than any of them.

I have very little concern for what a traditional systematist would say.

[Richard Norman]

On Thu, 04 Apr 2013 22:33:50 -0400, jillery <69jp...@gmail.com>
wrote:

I am not interested in titrating blame: X has 280495 units while Y
has only 280494 so X is the real culprit. No lie anywhere but you can
judge as you wish.

[John Harshman]

On 4/4/13 12:20 PM, pnyikos wrote:
> On Mar 29, 12:47 pm, John Harshman<jharsh...@pacbell.net> wrote:
>> On 3/29/13 9:26 AM, pnyikos wrote:
>>
>>> On Mar 29, 7:04 am, Ron O<rokim...@cox.net> wrote:
>
>>> This seems to be a recurring theme -- fossil evidence leading to
>>> opposite conclusions than genomic evidence. We saw it in the case
>>> where genomic evidence leads researchers to place the LCA of living
>>> placental (as opposed to marsupial, etc) mammals at ca. 105 mya, while
>>> fossil evidence was interpreted by them to place it past the K-T
>>> extinction event.
>>
>> It's a recurring theme only because you (and the world generally) take
>> note of the times it happens but not of the much more frequent times it
>> doesn't.
>
> Either that, or there are many other times having to do with closely
> related taxa, and so they escape notice.

I'm sticking with my interpretation until you give me reason to change
my mind.

> [For cladophiles like you, I
> should write "molecularly and morphologically similar" rather than
> "closely related" so as to make it intelligible to you.]

Sorry, but where are we supposed to make that substitution?

>> Man bites dog.
>
> Or maybe "cats bite hundreds of dogs, but it is only when man gets
> into the act that news reporters take notice."

No idea what the point was there.

>>> For more details, see:
>>
>>> http://groups.google.com/group/sci.bio.paleontology/msg/d0ec8fc6d5deed91
>>
>>>> The article is open access, but I wouldn't print it out. In
>>>> prepublication form it is over 70 pages.
>>
>>>> This turtle's genome appears to evolve more slowly than mammal
>>>> genomes. They claim a rate 1/3 of that of humans.
>>
>>> I wonder how they established this, and what the evidence would show
>>> as the rate of evolution of Sphenodon. Osteologically it is a "living
>>> fossil," hardly changed since Jurassic times.
>>
>> There is no apparent correlation, based on all sorts of data in all
>> sorts of taxa, between morphological and molecular evolutionary rates.
>
> However, I am still curious to know what the situation is with
> Sphenodon, as suggested in my first reply.

You must remain curious until there's a Sphenodon genome or a
substantial portion thereof. I'm just pointing out that there is no
reason to expect that there will be a correlation of its genetic
evolutionary rate with its morphological rate.

>> "How they established this" is presumably either by comparison of both
>> with outgroups ("relative rate test") or by using time-calibrated
>> phylogenies.
>
> The details would be nice to know.

So read the paper.

>>>> Also of interest
>>>> to this group is that they looked at the genes associated with teeth
>>>> (turtles lost their teeth) and found the same genes degenerating in
>>>> the genome as are found in birds. More evidence of common descent and
>>>> inheriting a genome from an ancestor with teeth.
>
> Yet another of millions of little nails in the coffin of creationism.
>
>>> If those same genes are found in Sphenodon, that could be significant.
>>
>> Surely that conclusion isn't controversial. Regardless of relationships,
>> both bird and turtle ancestors had teeth.
>
> Well, duh. I was interested in how much light the same genes in
> Sphenodon shed on what the LCA of extant Sauropsida was like.

"Like" in what way? We know what their teeth were like.

[Ron O]

On Apr 4, 9:50�pm, Richard Norman <r_s_nor...@comcast.net> wrote:
> On Thu, 04 Apr 2013 22:33:50 -0400, jillery <69jpi...@gmail.com>

> wrote:
>
>
>
>
>
>
>
>
>
> >On Thu, 04 Apr 2013 17:36:39 -0700, Richard Norman

> ><r_s_nor...@comcast.net> wrote:
>
> >>On Thu, 4 Apr 2013 16:52:30 -0700 (PDT), Ron O <rokim...@cox.net>

Ignorance really is bliss.

Ron Okimoto

[jillery]

On Thu, 04 Apr 2013 19:50:13 -0700, Richard Norman

If you really believe as you say, why do you not mete out your
consequences in the ratio of 280494:280495? How do you rationalize
letting Y have it all his way on the basis of less than one part in
200000? How is that not titrating blame? How is that evenhanded?

[jillery]

On Thu, 4 Apr 2013 20:00:29 -0700 (PDT), Ron O <roki...@cox.net>
wrote:

Speaking for myself, I regret these actions that have been directed
against you.

[Roger Shrubber]

On Apr 5, 2:38 pm, jillery <69jpi...@gmail.com> wrote:


> If you really believe as you say, why do you not mete out your
> consequences in the ratio of 280494:280495?  How do you rationalize
> letting Y have it all his way on the basis of less than one part in
> 200000?  How is that not titrating blame?  How is that evenhanded?

http://tinyurl.com/d6y6jbv
Count the number of individuals in each panel.
Identify the activity.

I happily delude myself to think I'm more of this:
http://tinyurl.com/bod8qod

[jillery]

I can imagine what I might mean with these images in this context, but
I try not to presume that's the same as what you mean. I can also
tell that you're being clever or subtle or both, so I won't spoil that
by asking you to spell it out.

[jillery]

On Fri, 05 Apr 2013 02:12:47 -0400, jillery <69jp...@gmail.com>
wrote:

But I will point out that with all the team dance competitions I have
seen, when one partner tangos badly, they make both partners leave.
Just sayin'.

[Ron O]

On Apr 4, 11:38�pm, jillery <69jpi...@gmail.com> wrote:
> On Thu, 04 Apr 2013 19:50:13 -0700, Richard Norman
>
>
>
>
>
>
>
>
>

> <r_s_nor...@comcast.net> wrote:
> >On Thu, 04 Apr 2013 22:33:50 -0400, jillery <69jpi...@gmail.com>

> >wrote:
>
> >>On Thu, 04 Apr 2013 17:36:39 -0700, Richard Norman

> >><r_s_nor...@comcast.net> wrote:
>
> >>>On Thu, 4 Apr 2013 16:52:30 -0700 (PDT), Ron O <rokim...@cox.net>

It isn't just that. He is so far off in his estimate that he is being
dishonest with himself. That is just a fact. Even if the ratio was
as close as 55:45 he would be so many orders of magnitude off that it
would be ridiculous. He should go back through Feb and March and
quantify the issue himself. Heck he can go back as far as he can
stand to do it. It is easy to go through my posts, but there are a
heck of a lot more Nyikos bogousity to wade through. January should
be easy because I don't recall much of an exchange between myself and
Nyikos and it was basically just Nyikos claiming that his knockdown
was going to be delayed until Feb. The rest of the whining and
bleating was Nyikos to other posters.

I realize that the squeaky wheel gets the grease and there is no
squeakier wheel on TO than Nyikos, but I don't participate in most of
that. It is all Nyikos bleating to himself. If anyone wants to
believe a liar like Nyikos I do feel sorry for them.

Ron Okimoto

[Ron O]

On Apr 5, 12:10�am, Roger Shrubber <rog.shrub...@gmail.com> wrote:
> On Apr 5, 2:38�pm, jillery <69jpi...@gmail.com> wrote:
>
> > If you really believe as you say, why do you not mete out your
> > consequences in the ratio of 280494:280495? �How do you rationalize
> > letting Y have it all his way on the basis of less than one part in
> > 200000? �How is that not titrating blame? �How is that evenhanded?
>
> http://tinyurl.com/d6y6jbv
> Count the number of individuals in each panel.
> Identify the activity.

I doubt that you believe this yourself. Just think about all the
times, just with you, that Nyikos has tangoed by himself about me.
Just think how often it happens with someone like Hashman and then
factor in everyone else. Really, how can you lie to yourself like
this? Just because you were wrong about it once doesn't mean that you
have to keep being wrong. What if I start claiming that if it wasn't
for guys like you Nyikos would have run out of steam by now and just
slithered away? He goes months without posting to me. That is just a
fact. What is he doing during those periods? Who is enabling that?
I'll give you a hint, it is not me.

Ron Okimoto

[Roger Shrubber]

When he rants about you, I think he is an idiot.
When you rant about him, I think you are an idiot.
Do you need another picture?

[jillery]

On Fri, 5 Apr 2013 04:20:18 -0700 (PDT), Ron O <roki...@cox.net>
wrote:

I agree with you. So if rnorman's reasoning doesn't wash even with
his own assessment of blame, it really falls apart against actual
reality.

[jillery]

I accept the above as a concise description of your perception of the
situation. With it, you imply their behaviors are equivalent and
indistinguishable, both in quantity or quality, the only functional
difference being in the names on their posts.

While I agree that a superficial or selective review of the evidence
might support your conclusion, I submit that a fuller analysis obliges
you to identify and distinguish the actions of the instigator from his
targets.

The immediate situation is made worse because Ron O. and other targets
are being held to account for their "egregious" behavior, while
rockhead's behavior is largely dismissed and ignored. He doesn't need
anyone's permission, only their tacit acceptance.

[Mark Isaak]

On 4/4/13 7:21 PM, Ron O wrote:
> On Apr 4, 7:36 pm, Richard Norman <r_s_nor...@comcast.net> wrote:
>> On Thu, 4 Apr 2013 16:52:30 -0700 (PDT), Ron O <rokim...@cox.net>
>> wrote:
>>> On Apr 4, 6:34 pm, Burkhard <b.scha...@ed.ac.uk> wrote:
>>>> On Apr 5, 12:04 am, Ron O <rokim...@cox.net> wrote:

>> [...]

In other words, because Nyikos's behavior is crappy, you choose to
engage in the same crappy behavior yourself. You want to be just like him.

--
Mark Isaak eciton (at) curioustaxonomy (dot) net
"It is certain, from experience, that the smallest grain of natural
honesty and benevolence has more effect on men's conduct, than the most
pompous views suggested by theological theories and systems." - D. Hume

[jillery]

The above is the standard reply to posters who challenge rockhead's
egregious behaviors. It presents a false and dishonest paraphrase of
the poster's statement, followed by a bald assertion that the poster's
behavior is functionally and morally equivalent to rockhead's.

Apparently everybody but rockhead agrees his behavior is crappy. So
the only thing worth discussing is how to deal with rockhead's crappy
behavior. Events over the past two years have shown that whatever
causes rockhead to behave badly is entirely independent of the
behaviors of other posters. Ignoring him only emboldens him.
Criticizing those who criticize rockhead enables him. Any effective
solution to rockhead's crappy behavior necessarily focuses on
rockhead's crappy behavior.

[Ron O]

So you do know how wrong you are. That is all that you had to say.
You know what Peter does so what is your excuse?

Ron Okimoto

[Ron O]

On Apr 5, 9:00�am, jillery <69jpi...@gmail.com> wrote:
> On Fri, 5 Apr 2013 04:20:18 -0700 (PDT), Ron O <rokim...@cox.net>

It really doesn't matter who is wrong about this. It is just a fact
that we all have to live with the plain and simple fact that Nyikos is
just a degenerate asshole. I don't blame anyone else for it. Reality
is just what it is. Beats me why people have to comment on it and be
so ignorant of the facts.

Ron Okimoto

[Paul J Gans]

Burkhard <b.sc...@ed.ac.uk> wrote:

>On Apr 5, 12:04?am, Ron O <rokim...@cox.net> wrote:


>> Nyikos can call this taunting, but he knows for a fact that it is all

>> true. ?So just deliver your third stupid knockdown and stop posting to

>> me like you said that you would over a year ago.
>>
>> Ron Okimoto

>Ok, that's it, and with some regret, as you on occasions post
>interesting stuff, but your pathological obsession makes the noise
>information ratio well below acceptable, not to mention lacking basic
>civility in posting. Plonk

Perhaps one has to be in the shoes of a target of Peter's in
order to understand pathological obsession. It is very simple
to hint that one should not respond to continuous taunts in
post after post, but very difficult to live with.

So I advocate mercy.

--
--- Paul J. Gans

[Ron O]

Pretty much the only thing that Nyikos understands and will leave me
alone for a bit. You have to demonstrate that he really is the
asshole that he himself understands himself to be.

Right now I am just pointing out to him that his bogus threats about
delivering the third knockdown never amounted to anything. He has
said that he will stop posting to me after the third one, but he keeps
putting it off. Not that I believe that he will do what he says. You
only have to realize that it has been a year and a half since he
started his stupid knockdown campaign and that his knockdowns were
supposed to come that long ago to know what Nyikos' promises are
worth.

Ron Okimoto

[Robert Camp]

My opinion, Ron, is that he really doesn't understand. He's missing
the bit of wiring that allows him to see himself as others see
him...to maintain a balanced perspective.

Surely you can see by now that nothing will be accomplished by taking
offense at someone who cannot help himself. When the interaction
descends from substance to squabbling, the only person your continued
involvement can reflect upon is you.

[Ron O]

On Apr 9, 12:09�ｿｽam, Robert Camp <robertlc...@hotmail.com> wrote:
> On Apr 5, 4:19�ｿｽpm, Ron O <rokim...@cox.net> wrote:

>
>
>
>
>
>
>
>
>
> > On Apr 5, 12:31�ｿｽpm, Mark Isaak <eci...@curioustax.onomy.net> wrote:
>
> > > On 4/4/13 7:21 PM, Ron O wrote:
>
> > > > On Apr 4, 7:36 pm, Richard Norman <r_s_nor...@comcast.net> wrote:
> > > >> On Thu, 4 Apr 2013 16:52:30 -0700 (PDT), Ron O <rokim...@cox.net>
> > > >> wrote:
> > > >>> On Apr 4, 6:34 pm, Burkhard <b.scha...@ed.ac.uk> wrote:
> > > >>>> On Apr 5, 12:04 am, Ron O <rokim...@cox.net> wrote:
> > > >> [...]
> > > >>>>> Nyikos can call this taunting, but he knows for a fact that it is all

> > > >>>>> true. �ｿｽSo just deliver your third stupid knockdown and stop posting to

> > > >>>>> me like you said that you would over a year ago.
>
> > > >>>>> Ron Okimoto
>
> > > >>>> Ok, that's it, and with some regret, as you on occasions post
> > > >>>> interesting stuff, but your pathological obsession makes the noise
> > > >>>> information ratio well below acceptable, not to mention lacking basic
> > > >>>> civility in posting. Plonk
>

> > > >>> I'm the one that has had enough. �ｿｽI still can't understand why anyone
> > > >>> would want to read junk that involves Nyikos. �ｿｽI stopped reading most

> > > >>> of the crap Nyikos posts 2 years ago.
>
> > > >> If you stopped reading it then how come you respond so vociferously

> > > >> and at such enormous length? �ｿｽWhy do you think we tolerate your crap
> > > >> about him any better than his rants? �ｿｽWhy don't both of you just give
> > > >> it a rest? �ｿｽEven one of you calling it quits would be an enormous
> > > >> improvement. �ｿｽNobody here would think the other would "win" just
> > > >> because there is no response. �ｿｽOn the contrary, we all would win by

> > > >> not being buried in this trash.
>
> > > >> That being said, this is an open news group and you can post whatever

> > > >> you wish consonant with or contrary to my advice. �ｿｽPlonk.

>
> > > > Why do you respond to any post?
>
> > > > If you read much of anything by Nyikos you likely know that most of

> > > > what he posts about me isn't to me. �ｿｽHasn't been since he went on his
> > > > knockdown bull pucky nearly a year and a half ago. �ｿｽWhat has Nyikos
> > > > been doing with respect to me in that year and a half? �ｿｽI have no

> > > > control over what Nyikos posts to anyone else, but when he posts his
> > > > crap to me I don't mind letting him know what a lowlife scum bag he

> > > > is. �ｿｽIt is the only thing that keeps him away for any length of time.

> > > > When he screws up really badly it will be months before he posts to me

> > > > again. �ｿｽThat is all that I can hope for. �ｿｽWhat has he been doing since
> > > > October and his last stupid knockdown attempt? �ｿｽBasically only whining
> > > > and bleating and claiming that his third knockdown is coming. �ｿｽThat is

> > > > all that I have had to put up with.
>
> > > In other words, because Nyikos's behavior is crappy, you choose to

> > > engage in the same crappy behavior yourself. �ｿｽYou want to be just like him.

>
> > Pretty much the only thing that Nyikos understands and will leave me

> > alone for a bit. �ｿｽYou have to demonstrate that he really is the

> > asshole that he himself understands himself to be.
>
> My opinion, Ron, is that he really doesn't understand. He's missing
> the bit of wiring that allows him to see himself as others see
> him...to maintain a balanced perspective.
>
> Surely you can see by now that nothing will be accomplished by taking
> offense at someone who cannot help himself. When the interaction
> descends from substance to squabbling, the only person your continued
> involvement can reflect upon is you.

There is no doubt that mental incompetence is a major factor in
Nyikos' problem, but he does understand just how degenerate and
dishonest he is. If he didn't he would not run from most of his
dishonest stupidity.

I took my own advice to Norman and started quantifying Nyikos' posts
that refer to me compared to posts that I post that refer to Nyikos.
I haven't gotten past the first thread that I chose where we are
exchanging posts the ratio is over 2 to 1, Nyikos compared to me. The
ratio isn't important not just because I haven't looked at threads
that I am not participating in, but in doing it I found some Nyikosian
claims that I had missed over the years. I don't really read much of
what Nyikos posts except what he posts to me, and I basically haven't
missed much except irritating bogus stupidity. There is no other word
for the Nykosian behavior. I found out that Nyikos claims to have
delivered his third knockdown, but he never informed me. He just made
the claim to some other poster several weeks ago. In reading our
exchanges in this thread, do you get any sense from Nyikos that Nyikos
has delivered his third knockdown and has claimed that he would stop
posting to me after doing such? Why does he keep pestering me? What
does Nyikos do instead of acknowledge that he has already supposedly
delivered his third knockdown? Nyikos obviously understand what a
loser he is. He is obviously a conniving lying scoundrel who knows
what he has done wrong, but has to lie about it. Pathetic is also a
word that I would use in describing such a person. What kind of
person would threaten and boast about the knockdowns that he was going
to deliver for a year and a half and then claim to deliver the last
one and slink away without telling the intended victim? That is
Nyikos, literally in a nutshell.

Ron Okimoto

[jillery]

On Tue, 9 Apr 2013 04:39:04 -0700 (PDT), Ron O <roki...@cox.net>
wrote:

>On Apr 9, 12:09�am, Robert Camp <robertlc...@hotmail.com> wrote:
>> On Apr 5, 4:19�pm, Ron O <rokim...@cox.net> wrote:

>>
>>
>>
>>
>>
>>
>>
>>
>>
>> > On Apr 5, 12:31�pm, Mark Isaak <eci...@curioustax.onomy.net> wrote:
>>
>> > > On 4/4/13 7:21 PM, Ron O wrote:
>>
>> > > > On Apr 4, 7:36 pm, Richard Norman <r_s_nor...@comcast.net> wrote:
>> > > >> On Thu, 4 Apr 2013 16:52:30 -0700 (PDT), Ron O <rokim...@cox.net>
>> > > >> wrote:
>> > > >>> On Apr 4, 6:34 pm, Burkhard <b.scha...@ed.ac.uk> wrote:
>> > > >>>> On Apr 5, 12:04 am, Ron O <rokim...@cox.net> wrote:
>> > > >> [...]
>> > > >>>>> Nyikos can call this taunting, but he knows for a fact that it is all

>> > > >>>>> true. �So just deliver your third stupid knockdown and stop posting to

>> > > >>>>> me like you said that you would over a year ago.
>>
>> > > >>>>> Ron Okimoto
>>
>> > > >>>> Ok, that's it, and with some regret, as you on occasions post
>> > > >>>> interesting stuff, but your pathological obsession makes the noise
>> > > >>>> information ratio well below acceptable, not to mention lacking basic
>> > > >>>> civility in posting. Plonk
>>

>> > > >>> I'm the one that has had enough. �I still can't understand why anyone
>> > > >>> would want to read junk that involves Nyikos. �I stopped reading most

>> > > >>> of the crap Nyikos posts 2 years ago.
>>
>> > > >> If you stopped reading it then how come you respond so vociferously

>> > > >> and at such enormous length? �Why do you think we tolerate your crap
>> > > >> about him any better than his rants? �Why don't both of you just give
>> > > >> it a rest? �Even one of you calling it quits would be an enormous
>> > > >> improvement. �Nobody here would think the other would "win" just
>> > > >> because there is no response. �On the contrary, we all would win by

>> > > >> not being buried in this trash.
>>
>> > > >> That being said, this is an open news group and you can post whatever

>> > > >> you wish consonant with or contrary to my advice. �Plonk.

>>
>> > > > Why do you respond to any post?
>>
>> > > > If you read much of anything by Nyikos you likely know that most of

>> > > > what he posts about me isn't to me. �Hasn't been since he went on his
>> > > > knockdown bull pucky nearly a year and a half ago. �What has Nyikos
>> > > > been doing with respect to me in that year and a half? �I have no

>> > > > control over what Nyikos posts to anyone else, but when he posts his
>> > > > crap to me I don't mind letting him know what a lowlife scum bag he

>> > > > is. �It is the only thing that keeps him away for any length of time.

>> > > > When he screws up really badly it will be months before he posts to me

>> > > > again. �That is all that I can hope for. �What has he been doing since
>> > > > October and his last stupid knockdown attempt? �Basically only whining
>> > > > and bleating and claiming that his third knockdown is coming. �That is

>> > > > all that I have had to put up with.
>>
>> > > In other words, because Nyikos's behavior is crappy, you choose to

>> > > engage in the same crappy behavior yourself. �You want to be just like him.

>>
>> > Pretty much the only thing that Nyikos understands and will leave me

>> > alone for a bit. �You have to demonstrate that he really is the

Yeppers. If he was actually treated as if he were an unsocialized
deaf, dumb, and blind child as Robert implies, there might be less of
a problem. But when he eats off my plate, I expect him to use his own
spoon, at the very least.

[Earle Jones]

In article
<8a9fcfed-a506-457e...@e5g2000yqa.googlegroups.com>,
Ron O <roki...@cox.net> wrote:

> On Apr 9, 12:09�am, Robert Camp <robertlc...@hotmail.com> wrote:
> > On Apr 5, 4:19�pm, Ron O <rokim...@cox.net> wrote:

> >
> >
> >
> >
> >
> >
> >
> >
> >
> > > On Apr 5, 12:31�pm, Mark Isaak <eci...@curioustax.onomy.net> wrote:
> >
> > > > On 4/4/13 7:21 PM, Ron O wrote:
> >
> > > > > On Apr 4, 7:36 pm, Richard Norman <r_s_nor...@comcast.net> wrote:
> > > > >> On Thu, 4 Apr 2013 16:52:30 -0700 (PDT), Ron O <rokim...@cox.net>
> > > > >> wrote:
> > > > >>> On Apr 4, 6:34 pm, Burkhard <b.scha...@ed.ac.uk> wrote:
> > > > >>>> On Apr 5, 12:04 am, Ron O <rokim...@cox.net> wrote:
> > > > >> [...]
> > > > >>>>> Nyikos can call this taunting, but he knows for a fact that it is
> > > > >>>>> all

> > > > >>>>> true. �So just deliver your third stupid knockdown and stop

> > > > >>>>> posting to
> > > > >>>>> me like you said that you would over a year ago.
> >
> > > > >>>>> Ron Okimoto
> >
> > > > >>>> Ok, that's it, and with some regret, as you on occasions post
> > > > >>>> interesting stuff, but your pathological obsession makes the noise
> > > > >>>> information ratio well below acceptable, not to mention lacking
> > > > >>>> basic
> > > > >>>> civility in posting. Plonk
> >

> > > > >>> I'm the one that has had enough. �I still can't understand why
> > > > >>> anyone
> > > > >>> would want to read junk that involves Nyikos. �I stopped reading

> > > > >>> most
> > > > >>> of the crap Nyikos posts 2 years ago.
> >
> > > > >> If you stopped reading it then how come you respond so vociferously

> > > > >> and at such enormous length? �Why do you think we tolerate your crap
> > > > >> about him any better than his rants? �Why don't both of you just
> > > > >> give
> > > > >> it a rest? �Even one of you calling it quits would be an enormous
> > > > >> improvement. �Nobody here would think the other would "win" just
> > > > >> because there is no response. �On the contrary, we all would win by

> > > > >> not being buried in this trash.
> >
> > > > >> That being said, this is an open news group and you can post
> > > > >> whatever

> > > > >> you wish consonant with or contrary to my advice. �Plonk.

> >
> > > > > Why do you respond to any post?
> >
> > > > > If you read much of anything by Nyikos you likely know that most of

> > > > > what he posts about me isn't to me. �Hasn't been since he went on his
> > > > > knockdown bull pucky nearly a year and a half ago. �What has Nyikos
> > > > > been doing with respect to me in that year and a half? �I have no

> > > > > control over what Nyikos posts to anyone else, but when he posts his
> > > > > crap to me I don't mind letting him know what a lowlife scum bag he

> > > > > is. �It is the only thing that keeps him away for any length of time.

> > > > > When he screws up really badly it will be months before he posts to
> > > > > me

> > > > > again. �That is all that I can hope for. �What has he been doing
> > > > > since
> > > > > October and his last stupid knockdown attempt? �Basically only
> > > > > whining
> > > > > and bleating and claiming that his third knockdown is coming. �That

> > > > > is
> > > > > all that I have had to put up with.
> >
> > > > In other words, because Nyikos's behavior is crappy, you choose to

> > > > engage in the same crappy behavior yourself. �You want to be just like

> > > > him.
> >
> > > Pretty much the only thing that Nyikos understands and will leave me

> > > alone for a bit. �You have to demonstrate that he really is the

*
Ron: Peter Nyikos is a puzzlement to me. I read all of the claims that
he is a "dishonest liar", but I never find any of his dishonest lies.

First of all, I don't read all the stuff. But a Phi Beta Kappa with a
PhD from Carnegie-Mellon, with all sorts of publications is not stupid.

He may be dishonest, but I have not noticed anything like that.

Maybe I have a soft spot in my heart (or maybe my head!) for math
teachers. I taught freshman math for four or five quarters at Georgia
Tech.

earle
*

[jillery]

Your lack of evidence may be a consequence of your own selection bias.
If you really wanted to find that evidence, you would have easily
found some from his posts of just this past week.

[Ron O]

On Apr 9, 6:46�pm, Earle Jones <earle.jo...@comcast.net> wrote:
> In article
> <8a9fcfed-a506-457e-9ae6-bba47e3e7...@e5g2000yqa.googlegroups.com>,

I'm not trying to knock you, but are you serious? It is difficult to
tell because Nyikos' difficulty with humor and irony is legendary. It
looks like you are making fun of the fact that one of Nyikos'
stupidest arguments defending himself against his incessant dishonesty
is that he is a professor of mathematics and has no reason to lie.

If you are not making fun of Nyikos I can provide multiple examples
with no problem. What is Nyikos doing in his post that led to this
discussion and why is he doing it?

http://groups.google.com/group/talk.origins/msg/6abfc8865e2638c0?hl=en

He is responding to this short post, so why did he delete what he
didn't want to deal with? Why not tell me that he had already claimed
to deliver his third knockdown several weeks ago, but had made the
claim to someone else and forgotten to tell his victim? It is a
stupid dishonesty that doesn't change reality, but Nyikos has to
retain his delusions, so he constantly lies to himself like this.
Nyikos has repeatedly made the claim that he would stop posting to me
after his third knockdown, but that doesn't seem to be the case here
or in other threads. He did put in the clause about reserving the
right to post to me, but why lie to himself like this?

QUOTE:

On Mar 29, 11:26 am, pnyikos <nyik...@bellsouth.net> wrote:

> On Mar 29, 7:04 am, Ron O <rokim...@cox.net> wrote:

Face it Nyikos about the only post that I want to see from you is your
third self inflicted knockdown post so that you will just leave me
alone. The knockdown never appeared in February like you claimed that
it would or in January like you claimed it would or soon after your
second stupidity last October.

What makes you think that I am at all interested in what you have to
post after your last assoholic episode? What a loser.

Ron Okimoto
END QUOTE:

This is the entire post that Nyikos is dishonestly running from, and
what does he have to do in order to lie to himself about running?

Ron Okimoto

[pnyikos]

John, this thread has been pretty well hijacked in talk.origins by
people making personal attacks, so I would like for us to move this on-
topic discussion to sci.bio.paleontology. There, the majority of
posts to this thread are still completely on-topic.

Accordingly, I've added s.b.p. to the newsgroups and will be making
on-topic comments after the attributions and earlier comments.

I'll see if I can interest Richard Norman in joining us over there.
His knowledge of paleontology could be of help.

On Apr 4, 10:50�pm, John Harshman <jharsh...@pacbell.net> wrote:

> On 4/4/13 11:54 AM, pnyikos wrote:

> > On Mar 29, 12:47 pm, John Harshman<jharsh...@pacbell.net> �wrote:

> >> On 3/29/13 9:26 AM, pnyikos wrote:
>
> >>> On Mar 29, 7:04 am, Ron O<rokim...@cox.net> � �wrote:

> >>>> Another interesting genome has been published. �It comes from the same
> >>>> lineage as crocs, dinos and birds.
>
> >>> This has been disputed by Gauthier and others, based on fossil
> >>> evidence. �They even dispute the claim that turtles are secondarily,
> >>> rather than primarily, anapsid. �If they are right, turtles are the
> >>> outliers of extant Sauropsida.
>
> >> If. The molecular data have been getting more and more conclusive in the
> >> past few years. Turtles are either archosaurs or the living sister group
> >> of archosaurs.

Still, Gauthier et. al. were holding out last year, according to the
article whose abstract Ron O linked:

21. Lyson TR, Sperling EA, Heimberg AM, Gauthier JA, King BL, Peterson
KJ:
MicroRNAs support a turtle plus lizard clade. Biol Lett 2012,
8:104-107.

-- http://genomebiology.com/content/pdf/gb-2013-14-3-r28.pdf

See also a comment about two total analyses from their webpage [posted
below]. But back to your last comment...

Is there actually molecular support for turtles being more closely
related to birds (in the cladistic sense) than to crocs??? That's
what it would take for molecular data to show that turtles are
archosaurs.

At the opposite extreme, as long as only fragments of the genome of
*Sphenodon* have been sequenced, it is too early to tell whether
turtles are the living sister group of archosaurs, even from a
molecular viewpoint.

> >> There is of course some morphological evidence that they are at least
> >> diapsids, mostly advanced by Olivier Rieppel and colleagues.
>
> > Not here, unless one of the co-authors here is a colleague:
>
> >>>>http://genomebiology.com/2013/14/3/R28/abstract
>
> > Are you referring to the papers listed in the following passage?
>
> > "The position of turtles (Testudines) is uncertain; some authors place
> > them approximately in the position shown above (Laurin& �Reisz, 1995;
> > Lee, 1993, 1995, 2001; Frost et al., 2006; Werneburg& �S nchez-
> > Villagra, 2009; Lyson et al. 2010), while others place them among
> > Diapsida (deBraga& �Rieppel, 1996, 1997; Rieppel& �Reisz, 1999; Hedges
> > & �Poling, 1999; Mannen& �Li, 1999; Hugall et al., 2007; Li et al.,
> > 2008)."
> > � �-- caption to phylogenetic tree of Amniota in
> > � �http://tolweb.org/Amniota/14990
>
> The ones by Rieppel are among the ones I was referring to.

Do you have a morphological analysis more recent than 1999 for turtles
being diapsids? Gauthier et. al. have more recent ones to point to,
including total analyses (see below).

> > The tree shows turtles (Testudines) in Anapsida.
>
> Since the various references conflict, they picked one over the others.

Seems they picked several 21st century ones over 20th century ones,
where morphology is concerned.

> > Laurin and Gauthier, who did the site, see your Rieppel et.al. ...1999
> > and raise it to 2010.
>
> > Later down in the page they write:
>
> > � "At least two total evidence analyses (in which molecular and
> > morphological data are combined) suggest that turtles are not diapsids
> > (Lee, 2001; Frost et al., 2006). In both, the molecular characters are
> > much more numerous than the morphological ones, which implies
> > significant support for the placement of turtles outside diapsids in
> > these molecular datasets."

Note the reasoning about the molecular evidence.

> > I wonder who is cherry-picking this time, you or they.
>
> Neither.

Why did you pick references from the 20th century, then? Was Rieppel
just the first author that popped into your mind?

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

[pnyikos]

CC: Richard Norman, because of the invitation below.

On Apr 4, 8:36锟絧m, Richard Norman <r_s_nor...@comcast.net> wrote:
> On Thu, 4 Apr 2013 16:52:30 -0700 (PDT), Ron O <rokim...@cox.net>
> wrote:

[huge snip]

> >I'm the one that has had enough. 锟絀 still can't understand why anyone

> >would want to read junk that involves Nyikos.

On this thread, it would presumably be the fact that I've kept on-
topic on this thread, except for one reply to Ron O. That continued
today with a reply I did to John Harshman a short while ago. It had
to do with the evidence of where turtles sit in Sauropsida-- diapsid
v. anapsid, archosaur v. sister group of archosaurs v. sister group of
{archosaurs, tuatara} v. Anapsida.

Richard, I was hoping you could join the two of us on this
discussion. With your knowledge of paleontology, I think you can be a
big help in discussing the morphological evidence, at least.

I've added sci.bio.paleontology to the newsgroups because (see my
reply to Harshman) this thread has been pretty well trashed by all the
personal attacks by others, and there we have a good chance of keeping
it on-topic. In fact, I wouldn't mind if you both started posting
just to s.b.p. I'll be watching for you over there.

> > 锟絀 stopped reading most

> >of the crap Nyikos posts 2 years ago.
>
> If you stopped reading it then how come you respond so vociferously

> and at such enormous length? 锟絎hy do you think we tolerate your crap
> about him any better than his rants? 锟絎hy don't both of you just give
> it a rest? 锟紼ven one of you calling it quits would be an enormous
> improvement.

I've done the nearest thing to that which I comfortably can. On the
"By Their Fruits...." thread I've told Hemidactylus about my new
policy. I gave him an almost complete statement of it, as follows:

"from now on, I will confine myself to very
brief direct replies to posts of Ron O,"

--http://groups.google.com/group/talk.origins/msg/5ec655abe34712f9

I carelessly left off a conditional bit ("in reply to me") that I had
put in a much earlier post to Hemidactylus:

"But after the third knockdown, I will reply to almost
nothing Ron O posts in reply to me..."

-- http://groups.google.com/group/talk.origins/msg/d319bac1c0c85623

Note: "almost nothing," not "almost no posts". That could come
later, if enough people become aware of my new policy. Everyone on
this thread seems to be oblivious to it so far, despite my hewing to
it in the one off-topic post I've done to this thread so far.

Peter Nyikos

[jillery]

On Wed, 10 Apr 2013 09:07:03 -0700 (PDT), pnyikos
<nyi...@bellsouth.net> wrote:

>John, this thread has been pretty well hijacked in talk.origins by
>people making personal attacks, so I would like for us to move this on-
>topic discussion to sci.bio.paleontology. There, the majority of
>posts to this thread are still completely on-topic.
>
>Accordingly, I've added s.b.p. to the newsgroups and will be making
>on-topic comments after the attributions and earlier comments.
>
>I'll see if I can interest Richard Norman in joining us over there.
>His knowledge of paleontology could be of help.

The above is quite ironic, since it was Ron O. who started this topic
in T.O. Which make you the hijacker.

[...]

[Richard Norman]

On Wed, 10 Apr 2013 09:07:03 -0700 (PDT), pnyikos
<nyi...@bellsouth.net> wrote:

>John, this thread has been pretty well hijacked in talk.origins by
>people making personal attacks, so I would like for us to move this on-
>topic discussion to sci.bio.paleontology. There, the majority of
>posts to this thread are still completely on-topic.
>
>Accordingly, I've added s.b.p. to the newsgroups and will be making
>on-topic comments after the attributions and earlier comments.
>
>I'll see if I can interest Richard Norman in joining us over there.
>His knowledge of paleontology could be of help.
>

<snip on topic discussion>

I actually have virtually no knowledge of paleontology. I am just an
interested observer with some knowledge of biology and the ability to
read the literature with a bit of understanding.

Yes I have enjoyed following your back-and-forths with John and have
not participated because I felt I had no useful information to add.
But I will pipe in when I think it useful or if I have questions of my
own.

About the "hijacking", I am responding to you separately.

[John Harshman]

Nope. A hijacker is a person who changes the subject. Peter is on-topic
here.

[John Harshman]

On 4/10/13 9:36 AM, pnyikos wrote:
> CC: Richard Norman, because of the invitation below.
>

> On Apr 4, 8:36 pm, Richard Norman<r_s_nor...@comcast.net> wrote:
>> On Thu, 4 Apr 2013 16:52:30 -0700 (PDT), Ron O<rokim...@cox.net>
>> wrote:
> [huge snip]
>

>>> I'm the one that has had enough. I still can't understand why anyone

>>> would want to read junk that involves Nyikos.
>
> On this thread, it would presumably be the fact that I've kept on-
> topic on this thread, except for one reply to Ron O.

And, of course, this one.

[John Harshman]

On 4/10/13 9:07 AM, pnyikos wrote:
> John, this thread has been pretty well hijacked in talk.origins by
> people making personal attacks, so I would like for us to move this on-
> topic discussion to sci.bio.paleontology. There, the majority of
> posts to this thread are still completely on-topic.
>
> Accordingly, I've added s.b.p. to the newsgroups and will be making
> on-topic comments after the attributions and earlier comments.

Sure. But all you will achieve with this is to fill s.b.p. with
off-topic posts. Better if you just ignored the off-topic bits. I
realize that you are constitutionally unable to do so, but perhaps you
could at least try.

> I'll see if I can interest Richard Norman in joining us over there.
> His knowledge of paleontology could be of help.
>
> On Apr 4, 10:50 pm, John Harshman<jharsh...@pacbell.net> wrote:
>> On 4/4/13 11:54 AM, pnyikos wrote:
>
>>> On Mar 29, 12:47 pm, John Harshman<jharsh...@pacbell.net> wrote:
>>>> On 3/29/13 9:26 AM, pnyikos wrote:
>>
>>>>> On Mar 29, 7:04 am, Ron O<rokim...@cox.net> wrote:
>>>>>> Another interesting genome has been published. It comes from the same
>>>>>> lineage as crocs, dinos and birds.
>>
>>>>> This has been disputed by Gauthier and others, based on fossil
>>>>> evidence. They even dispute the claim that turtles are secondarily,
>>>>> rather than primarily, anapsid. If they are right, turtles are the
>>>>> outliers of extant Sauropsida.
>>
>>>> If. The molecular data have been getting more and more conclusive in the
>>>> past few years. Turtles are either archosaurs or the living sister group
>>>> of archosaurs.
>
> Still, Gauthier et. al. were holding out last year, according to the
> article whose abstract Ron O linked:
>
> 21. Lyson TR, Sperling EA, Heimberg AM, Gauthier JA, King BL, Peterson
> KJ:
> MicroRNAs support a turtle plus lizard clade. Biol Lett 2012,
> 8:104-107.
>
> -- http://genomebiology.com/content/pdf/gb-2013-14-3-r28.pdf

So there were holdouts. How does that affect my point?

> See also a comment about two total analyses from their webpage [posted
> below]. But back to your last comment...
>
> Is there actually molecular support for turtles being more closely
> related to birds (in the cladistic sense) than to crocs??? That's
> what it would take for molecular data to show that turtles are
> archosaurs.

Yes. The molecular data are currently unable to distinguish between the
two hypotheses.

> At the opposite extreme, as long as only fragments of the genome of
> *Sphenodon* have been sequenced, it is too early to tell whether
> turtles are the living sister group of archosaurs, even from a
> molecular viewpoint.

Only if you think there's some chance that Sphenodon is the sister group
of archosaurs. Do you have any basis for such a belief? If not, why is
Sphenodon relevant?

>>>> There is of course some morphological evidence that they are at least
>>>> diapsids, mostly advanced by Olivier Rieppel and colleagues.
>>
>>> Not here, unless one of the co-authors here is a colleague:
>>
>>>>>> http://genomebiology.com/2013/14/3/R28/abstract
>>
>>> Are you referring to the papers listed in the following passage?
>>
>>> "The position of turtles (Testudines) is uncertain; some authors place
>>> them approximately in the position shown above (Laurin& Reisz, 1995;
>>> Lee, 1993, 1995, 2001; Frost et al., 2006; Werneburg& S nchez-
>>> Villagra, 2009; Lyson et al. 2010), while others place them among
>>> Diapsida (deBraga& Rieppel, 1996, 1997; Rieppel& Reisz, 1999; Hedges
>>> & Poling, 1999; Mannen& Li, 1999; Hugall et al., 2007; Li et al.,
>>> 2008)."
>>> -- caption to phylogenetic tree of Amniota in
>>> http://tolweb.org/Amniota/14990
>>
>> The ones by Rieppel are among the ones I was referring to.
>
> Do you have a morphological analysis more recent than 1999 for turtles
> being diapsids? Gauthier et. al. have more recent ones to point to,
> including total analyses (see below).

I don't, offhand.

>>> The tree shows turtles (Testudines) in Anapsida.
>>
>> Since the various references conflict, they picked one over the others.
>
> Seems they picked several 21st century ones over 20th century ones,
> where morphology is concerned.

Later isn't necessarily better. At any rate, the molecular data are
conclusive.

>>> Laurin and Gauthier, who did the site, see your Rieppel et.al. ...1999
>>> and raise it to 2010.
>>
>>> Later down in the page they write:
>>
>>> "At least two total evidence analyses (in which molecular and
>>> morphological data are combined) suggest that turtles are not diapsids
>>> (Lee, 2001; Frost et al., 2006). In both, the molecular characters are
>>> much more numerous than the morphological ones, which implies
>>> significant support for the placement of turtles outside diapsids in
>>> these molecular datasets."
>
> Note the reasoning about the molecular evidence.

Poor reasoning. There is either significant support or lots of noise or
lots of uninformative characters. Or some combination. At any rate, the
molecular data have continued to expand at high speed, to the point
where any combined analysis will merely echo the molecular tree.

>>> I wonder who is cherry-picking this time, you or they.
>>
>> Neither.
>
> Why did you pick references from the 20th century, then? Was Rieppel
> just the first author that popped into your mind?

Rieppel is the person who first raised the hypothesis. I haven't
followed what he's done with it recently.

[Richard Norman]

<snip remainder>

Quite frankly, you have not done the nearest thing which you can. You
should simply quit all that crap even if it gives you great
discomfort. You have the ability to dredge up all sorts of old
grudges and grievances and the ability to scrape open old wounds. You
also demonstrate that ability at enormous length and high frequency.
Please just give it up.

It doesn't matter if you have actually been aggrieved or whether you
simply perceive yourself aggrieved or whether you are just paranoid
and are making it all up. If people call you liar or worse and insult
you, then just let it lie. Those posts reflect more on their authors
and not on you. Your responses, even responses in kind and responses
you truly believe well justified , all those reflect on you and not to
your benefit.

Please do NOT respond to me by citing all the instances of when you
were insulted and "took the high road" only to be rebuffed or
whatever. Please especially do NOT tell me about all the terrible
things Ron O or others may have done to you and how you responded.
Please DO just let it drop. Bite your tongue, have a stiff drink,
yell at your dog -- whatever. But just keep your fingers off the
keyboard.

You do show interest in participating in real discussions, whether
about vertebrate evolution or directed panspermia. I may strongly
disagree with you about some of these issues and think you are way off
base. But once the discussion deviates from the subject matter and
turns to the personality and motivation of the people posting then it
is time to simply quit. Nobody will think "the other guy won because
you can't respond." People will only think "that God that's stopped."

[jillery]

The OP is the one to say what the subject is and where the topic
should be discussed.

[John Harshman]

That's an interesting idea, but I don't think it's true. There is really
no ownership in usenet. Nobody decides, or perhaps everybody decides. I
think Peter was on-topic there, since he was talking about turtle
relationships, something that was also discussed in the original post.
You may think it isn't on-topic, but I would like to know your reasoning.

[Richard Norman]

On Wed, 10 Apr 2013 13:28:29 -0700, John Harshman

Ron O did start the thread on the turtle genome and named it just that
in the subject line. Peter responded in kind about the turtle and had
a discussion quite on topic with John. Ron O immediately responded to
Peter's post with an attack on Peter. Can you hijack your own thread?
I think so.

I would prefer to return to the topic and so I ask John why
"traditional systematists" are held in such low regard. Isn't this
just a typical arrogance of the molecular people when there is
disagreement about lineage? Is there a consensus about turtles or is
there really some debate?

[John Harshman]

No. "Traditional systematists" doesn't refer to morphological
systematists but to those who prefer grades to clades, e.g. Ernst Mayr
and his (mostly also dead) compatriots. As for the arrogance of the
molecular people, it's by this point pretty well deserved. There's a lot
more data in the genome than elsewhere, and a lot more data in extant
species than in fossils.

> Is there a consensus about turtles or is
> there really some debate?

There ought to be a consensus, but there isn't yet, as far as I know.
Then again it took a good 35 years (and counting) to get a consensus on
a matter so simple as the relationships of gharials, despite the data.

[alias Ernest Major]

I think you'll find that it's not morphological vs molecular, but
traditional vs cladistic. (I'm all that sure of the low regard either.)

The problem with traditional systematics is baseing classifications on a
small number of subjectively selected "key" characters, rather than on
all the evidence. Traditional systematists had the excuse that they had
less data to work on, and less computational resources with which to
analyse that data that they did have.

And on the other hand one can criticise equal weighted maximum parsimony
as a technique - it leads to papers claiming that flight (re-)evolved n
times in stick insects, rather than being lost n+1 times. How to weight
traits is a difficult question to answer, but weighting them all the
same is clearly at best a simplifying approximation. And selecting the
traits to use in an analysis remains a subjective process, leading
cherry picking still being a hazard.

--
alias Ernest Major

[John Harshman]

That wasn't quite the "traditional" that Peter was talking about. He was
referring, essentially, to gradism.

> And on the other hand one can criticise equal weighted maximum parsimony
> as a technique - it leads to papers claiming that flight (re-)evolved n
> times in stick insects, rather than being lost n+1 times.

Oh, now, be fair. They had a likelihood model that gave them the same
result, though I never quite understood why.

> How to weight
> traits is a difficult question to answer, but weighting them all the
> same is clearly at best a simplifying approximation. And selecting the
> traits to use in an analysis remains a subjective process, leading
> cherry picking still being a hazard.

And, as in your stick insect example, the assumption of symmetrical
transition probabilities may be unwarranted too.

[pnyikos]

Taking a short breather from the grading of tests...

On Apr 10, 5:46�pm, John Harshman <jharsh...@pacbell.net> wrote:
> On 4/10/13 2:34 PM, alias Ernest Major wrote:

> > On 10/04/2013 21:56, Richard Norman wrote:


> >> I would prefer to return to the topic and so I ask John why
> >> "traditional systematists" are held in such low regard. Isn't this
> >> just a typical arrogance of the molecular people when there is
> >> disagreement about lineage? Is there a consensus about turtles or is
> >> there really some debate?
>
> > I think you'll find that it's not morphological vs molecular, but
> > traditional vs cladistic. (I'm all that sure of the low regard either.)

I think it is molecular vs. morphological that takes into account
extinct taxa, like *Eusthenopteron*.

> > The problem with traditional systematics is baseing classifications on a
> > small number of subjectively selected "key" characters, rather than on
> > all the evidence.

Largely true, but subjectivity is in the eye of the beholder.

For instance, I've said in the past that just the structure of the
shoulder girdle in the monotremes vs. marsupials and placentals should
outweigh a really hefty number of minor (especially molecular)
characters as far as what is the sister group of what.

The scapula of marsupials and placentals is essentially identical,
even to a raised median ridge, while that of monotremes is utterly
different. Also there is at least one extra element in the monotreme
shoulder girdle.

Harshman's reply was a dismissive "If only it were that simple". Had
I said "all" except "a really hefty" [actually, words to that effect]
he would have been on target. Instead I think it would have been more
appropriate for him to say "I'm glad the process we use is not so
complicated."

[snip]

> That wasn't quite the "traditional" that Peter was talking about. He was
> referring, essentially, to gradism.

If you are referring to grades as in "subholostean grade" and
"holostean grade" you are dead wrong. That is the only example of
polyphyletic taxon that Romer gave in _Vertebrate Paleontology_, the
example of both the bowfin and the gar being in Holostei.

What I keep referring to is the traditional Linnean classification
whereby every organism had its own genus, family, order etc.
[including some intermediates like "suborder," "infraorder,"
"superfamily" in some cases]. Cladistic classification is great for
extant taxa, but the further back in time one goes, the more
unsatisfactory it is.

In guides to mushrooms, trees, etc. one has means of identification
for non-specialists that classifies things according to spore print
and other visible characters. If a fossil has the various apomorpies
that narrow down its clade missing, at least the Linnean
classification gave other ready criteria for identifying it, or at
least narrowing it down to the smallest feasible Linnean taxon.

> > And on the other hand one can criticise equal weighted maximum parsimony
> > as a technique - it leads to papers claiming that flight (re-)evolved n
> > times in stick insects, rather than being lost n+1 times.

I'm unfamilar with that example, but see above about radically
different weightings. Another example is megabats v. microbats. A
look at how the two inner digits of the wings are close together in
both, as well as the whole overall shape of the wings, should have
made everyone treat the hypothesis that they evolved flight separately
with the formula, "Extraordinary claims require extraordinary
evidence."

Ditto the claim that marsupials are sister group to
{placentals ,monotremes}.

> Oh, now, be fair. They had a likelihood model that gave them the same
> result, though I never quite understood why.
>
> > How to weight
> > traits is a difficult question to answer, but weighting them all the
> > same is clearly at best a simplifying approximation.

At worst, it is pseudoscience.

> > And selecting the
> > traits to use in an analysis remains a subjective process, leading
> > cherry picking still being a hazard.

I confine myself to clear cut cases like the two I've given above and
in the past.

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

[pnyikos]

On Apr 10, 6:30�pm, pnyikos <nyik...@bellsouth.net> wrote:
> Taking a short breather from the grading of tests...
>
> On Apr 10, 5:46 pm, John Harshman <jharsh...@pacbell.net> wrote:
>
> > On 4/10/13 2:34 PM, alias Ernest Major wrote:
> > > I think you'll find that it's not morphological vs molecular, but
> > > traditional vs cladistic. (I'm all that sure of the low regard either.)
>
> I think it is molecular vs. morphological that takes into account
> extinct taxa, like *Eusthenopteron*.

Ouch! I meant *Eunotosaurus*.

It's been a long day already. :-(

[John Harshman]

On 4/10/13 3:30 PM, pnyikos wrote:
> Taking a short breather from the grading of tests...
>
> On Apr 10, 5:46 pm, John Harshman<jharsh...@pacbell.net> wrote:
>> On 4/10/13 2:34 PM, alias Ernest Major wrote:
>
>>> On 10/04/2013 21:56, Richard Norman wrote:
>
>
>>>> I would prefer to return to the topic and so I ask John why
>>>> "traditional systematists" are held in such low regard. Isn't this
>>>> just a typical arrogance of the molecular people when there is
>>>> disagreement about lineage? Is there a consensus about turtles or is
>>>> there really some debate?
>>
>>> I think you'll find that it's not morphological vs molecular, but
>>> traditional vs cladistic. (I'm all that sure of the low regard either.)
>
> I think it is molecular vs. morphological that takes into account
> extinct taxa, like *Eusthenopteron*.

Then you are wrong. I think you're confusing the discussion of turtle
cladistic relationships (not traditional systematics) with your ideas of
close relationships to ancestors (traditional).

>>> The problem with traditional systematics is baseing classifications on a
>>> small number of subjectively selected "key" characters, rather than on
>>> all the evidence.
>
> Largely true, but subjectivity is in the eye of the beholder.
>
> For instance, I've said in the past that just the structure of the
> shoulder girdle in the monotremes vs. marsupials and placentals should
> outweigh a really hefty number of minor (especially molecular)
> characters as far as what is the sister group of what.
>
> The scapula of marsupials and placentals is essentially identical,
> even to a raised median ridge, while that of monotremes is utterly
> different. Also there is at least one extra element in the monotreme
> shoulder girdle.
>
> Harshman's reply was a dismissive "If only it were that simple". Had
> I said "all" except "a really hefty" [actually, words to that effect]
> he would have been on target. Instead I think it would have been more
> appropriate for him to say "I'm glad the process we use is not so
> complicated."

We'll all do better if you stop these retrospective judgments rendered
to third parties.

>> That wasn't quite the "traditional" that Peter was talking about. He was
>> referring, essentially, to gradism.
>
> If you are referring to grades as in "subholostean grade" and
> "holostean grade" you are dead wrong. That is the only example of
> polyphyletic taxon that Romer gave in _Vertebrate Paleontology_, the
> example of both the bowfin and the gar being in Holostei.
>
> What I keep referring to is the traditional Linnean classification
> whereby every organism had its own genus, family, order etc.
> [including some intermediates like "suborder," "infraorder,"
> "superfamily" in some cases]. Cladistic classification is great for
> extant taxa, but the further back in time one goes, the more
> unsatisfactory it is.

You have confused cladistic classification with unranked classification.
It's possible to have a cladistic, Linnean classification. And of course
you like the traditional classification because it's all about grades.

> In guides to mushrooms, trees, etc. one has means of identification
> for non-specialists that classifies things according to spore print
> and other visible characters. If a fossil has the various apomorpies
> that narrow down its clade missing, at least the Linnean
> classification gave other ready criteria for identifying it, or at
> least narrowing it down to the smallest feasible Linnean taxon.

Not really, no.

>>> And on the other hand one can criticise equal weighted maximum parsimony
>>> as a technique - it leads to papers claiming that flight (re-)evolved n
>>> times in stick insects, rather than being lost n+1 times.
>
> I'm unfamilar with that example, but see above about radically
> different weightings. Another example is megabats v. microbats. A
> look at how the two inner digits of the wings are close together in
> both, as well as the whole overall shape of the wings, should have
> made everyone treat the hypothesis that they evolved flight separately
> with the formula, "Extraordinary claims require extraordinary
> evidence."
>
> Ditto the claim that marsupials are sister group to
> {placentals ,monotremes}.
>
>> Oh, now, be fair. They had a likelihood model that gave them the same
>> result, though I never quite understood why.
>>
>>> How to weight
>>> traits is a difficult question to answer, but weighting them all the
>>> same is clearly at best a simplifying approximation.
>
> At worst, it is pseudoscience.

Why?

>>> And selecting the
>>> traits to use in an analysis remains a subjective process, leading
>>> cherry picking still being a hazard.
>
> I confine myself to clear cut cases like the two I've given above and
> in the past.

If only it were that simple, to coin a phrase.

[Richard Norman]

I do not understand why your selection of morphologial characters
should have more weight than somebody elses. You say you have reasons
but then so does everybody else. In other words, it really isn't that
simple.

You may confine yourself to clear cut cases (whether the two you gave
are such is another problem) but isn't that a form of cherry picking?
You simply abandon anything tricky?

And "traditional" classification is more than Linnean categories. I
think a good example of grades is given by the quite traditional
notion of acoelomate, pseudocoelomate, and coelomate kinds of
protostome. Or non-vascular vs. vascular plants. But then I am not a
systemacist so I am not in a position to say what specialists in this
area consider "traditional" just as I am not in a position to evaluate
why this particular feature should count with heavier weight than that
one. I do know that counting as separate features those that are
really highly correlated by one developmental process is flawed.

[jillery]

On Wed, 10 Apr 2013 13:28:29 -0700, John Harshman

If there is no ownership, then nobody has the authority to move the
topic to a different newsgroup.

Since the topic is "turtle genome sequence", the topic is explicitly
*not* "this thread has been pretty well hijacked in talk.origins by
people making personal attacks." So how you can say his comments
above are on-topic is beyond me.

You made substantially the same point here:

<rNKdnSEEZLS...@giganews.com>

so why you challenge me about it makes no sense. It's as if you think
only you have the authority to criticize him.

[Richard Norman]

On Wed, 10 Apr 2013 21:53:24 -0400, jillery <69jp...@gmail.com>

So where do you stand on the group once called "Anapsida"? Do holes
in the skull count for anything anymore?

[Glenn]

"jillery" <69jp...@gmail.com> wrote in message news:ij5cm8d14emn4gcq4...@4ax.com...

Off with their heads!

[John Harshman]

Or perhaps anybody has the authority.

> Since the topic is "turtle genome sequence", the topic is explicitly
> *not* "this thread has been pretty well hijacked in talk.origins by
> people making personal attacks." So how you can say his comments
> above are on-topic is beyond me.

I was referring to the on-topic comments that were also in the post.

> You made substantially the same point here:
>
> <rNKdnSEEZLS...@giganews.com>
>
> so why you challenge me about it makes no sense. It's as if you think
> only you have the authority to criticize him.

No authority is needed. But in fact most of his post was on-topic.

[jillery]

On Wed, 10 Apr 2013 19:16:58 -0700, Richard Norman
<r_s_n...@comcast.net> wrote:

[...]

>So where do you stand on the group once called "Anapsida"? Do holes
>in the skull count for anything anymore?

I am no expert, but an interested observer, apparently like you. I
understand that in the past they had to rely on morphological
differences. It's reasonable to expect temporal fenestrae to be a
reliable indicator of lineage.

But I also recognize that morphological interpretation can be
subjective and not detailed enough to distinguish many cases. All
other things being equal, I would bet on the genetic data. So a
question in my mind is what evolutionary process drove turtles to
revert to the primitive form? Perhaps it had something to do with the
development of their shells, but that's just speculation.

[eridanus]

El martes, 9 de abril de 2013 12:39:04 UTC+1, Ron O escribi�ｿｽ:
> On Apr 9, 12:09�ｿｽam, Robert Camp <robertlc...@hotmail.com> wrote:
>
> > On Apr 5, 4:19�ｿｽpm, Ron O <rokim...@cox.net> wrote:

>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> >
>
> > > On Apr 5, 12:31�ｿｽpm, Mark Isaak <eci...@curioustax.onomy.net> wrote:
>
> >
>
> > > > On 4/4/13 7:21 PM, Ron O wrote:
>
> >
>

> > > > > On Apr 4, 7:36 pm, Richard Norman <r_s_nor...@comcast.net> wrote:
>
> > > > >> On Thu, 4 Apr 2013 16:52:30 -0700 (PDT), Ron O <rokim...@cox.net>
>
> > > > >> wrote:
>

> > > > >>> On Apr 4, 6:34 pm, Burkhard <b.scha...@ed.ac.uk> wrote:
>
> > > > >>>> On Apr 5, 12:04 am, Ron O <rokim...@cox.net> wrote:
>
> > > > >> [...]
>
> > > > >>>>> Nyikos can call this taunting, but he knows for a fact that it is all
>

> > > > >>>>> true. �ｿｽSo just deliver your third stupid knockdown and stop posting to

>
> > > > >>>>> me like you said that you would over a year ago.
>
> >
>
> > > > >>>>> Ron Okimoto
>
> >
>
> > > > >>>> Ok, that's it, and with some regret, as you on occasions post
>
> > > > >>>> interesting stuff, but your pathological obsession makes the noise
>
> > > > >>>> information ratio well below acceptable, not to mention lacking basic
>
> > > > >>>> civility in posting. Plonk
>
> >
>

> > > > >>> I'm the one that has had enough. �ｿｽI still can't understand why anyone
>
> > > > >>> would want to read junk that involves Nyikos. �ｿｽI stopped reading most

>
> > > > >>> of the crap Nyikos posts 2 years ago.
>
> >
>
> > > > >> If you stopped reading it then how come you respond so vociferously
>

> > > > >> and at such enormous length? �ｿｽWhy do you think we tolerate your crap
>
> > > > >> about him any better than his rants? �ｿｽWhy don't both of you just give
>
> > > > >> it a rest? �ｿｽEven one of you calling it quits would be an enormous
>
> > > > >> improvement. �ｿｽNobody here would think the other would "win" just
>
> > > > >> because there is no response. �ｿｽOn the contrary, we all would win by

>
> > > > >> not being buried in this trash.
>
> >
>
> > > > >> That being said, this is an open news group and you can post whatever
>

> > > > >> you wish consonant with or contrary to my advice. �ｿｽPlonk.

>
> >
>
> > > > > Why do you respond to any post?
>
> >
>
> > > > > If you read much of anything by Nyikos you likely know that most of
>

> > > > > what he posts about me isn't to me. �ｿｽHasn't been since he went on his
>
> > > > > knockdown bull pucky nearly a year and a half ago. �ｿｽWhat has Nyikos
>
> > > > > been doing with respect to me in that year and a half? �ｿｽI have no

>
> > > > > control over what Nyikos posts to anyone else, but when he posts his
>
> > > > > crap to me I don't mind letting him know what a lowlife scum bag he
>

> > > > > is. �ｿｽIt is the only thing that keeps him away for any length of time.

>
> > > > > When he screws up really badly it will be months before he posts to me
>

> > > > > again. �ｿｽThat is all that I can hope for. �ｿｽWhat has he been doing since
>
> > > > > October and his last stupid knockdown attempt? �ｿｽBasically only whining
>
> > > > > and bleating and claiming that his third knockdown is coming. �ｿｽThat is

>
> > > > > all that I have had to put up with.
>
> >
>
> > > > In other words, because Nyikos's behavior is crappy, you choose to
>

> > > > engage in the same crappy behavior yourself. �ｿｽYou want to be just like him.

>
> >
>
> > > Pretty much the only thing that Nyikos understands and will leave me
>

> > > alone for a bit. �ｿｽYou have to demonstrate that he really is the

he is not aware of that he is stupid because for he has a PhD
tittle of something. So, any ass with a title is not aware of
being an ass. Just imagine that he has been possessed by the holy
ghost to preach the gospel of panespermia. It is clinical case.
It is a little like Jim Jones of the Guyana, but he has not the
enough followers. Think that he is the Messiah. This would explain
his behavior. You cannot argue with the Messiah.

Eridanus

[*Hemidactylus*]

On 04/11/2013 06:34 AM, eridanus wrote:

[snip]

> he is not aware of that he is stupid because for he has a PhD
> tittle of something. So, any ass with a title is not aware of
> being an ass. Just imagine that he has been possessed by the holy
> ghost to preach the gospel of panespermia. It is clinical case.
> It is a little like Jim Jones of the Guyana, but he has not the
> enough followers. Think that he is the Messiah. This would explain
> his behavior. You cannot argue with the Messiah.

The Jim Jones remark was a bit gratuitous doncha think, conjuring up
very tragic images for rhetorical effect? Besides, if he's in your
estimation a charismatic messiah type looking to recruit followers, he's
going about that in an unsuccessful manner. I just don't see it.

I see someone cornered and beset who is lashing back at a mob. Did he
help get himself in that corner? Perhaps. Should the mob continue the
beat down? Nope.

[jillery]

On Wed, 10 Apr 2013 22:07:28 -0700, John Harshman

You conflate power with authority. Since you deny it, then how about
simple courtesy and a common sense application of the golden rule? One
could easily start a parallel topic in a different newsgroup, so
there's no need to move an exisiting one.

>> Since the topic is "turtle genome sequence", the topic is explicitly
>> *not* "this thread has been pretty well hijacked in talk.origins by
>> people making personal attacks." So how you can say his comments
>> above are on-topic is beyond me.
>
>I was referring to the on-topic comments that were also in the post.

In your post to which I replied, you make no such reference.

>> You made substantially the same point here:
>>
>> <rNKdnSEEZLS...@giganews.com>
>>
>> so why you challenge me about it makes no sense. It's as if you think
>> only you have the authority to criticize him.
>
>No authority is needed. But in fact most of his post was on-topic.

So you contradict yourself. No surprise there.

[jillery]

My recollection may be in error, but I don't recall you expressing
such sympathies for other victims of "the mob". Is it your opinion
that he is uniquely beset?

[John Harshman]

In fact, nobody has moved anything, if you will notice. Peter merely
added s.b.p. to the newsgroups list. This is something worth arguing about?

>>> Since the topic is "turtle genome sequence", the topic is explicitly
>>> *not* "this thread has been pretty well hijacked in talk.origins by
>>> people making personal attacks." So how you can say his comments
>>> above are on-topic is beyond me.
>>
>> I was referring to the on-topic comments that were also in the post.
>
> In your post to which I replied, you make no such reference.

Didn't think an explicit reference was necessary, since you were
presumably capable of reading the parts of Peters post you deleted.

>>> You made substantially the same point here:
>>>
>>> <rNKdnSEEZLS...@giganews.com>
>>>
>>> so why you challenge me about it makes no sense. It's as if you think
>>> only you have the authority to criticize him.
>>
>> No authority is needed. But in fact most of his post was on-topic.
>
> So you contradict yourself. No surprise there.

You have an odd tendency to find what isn't there. Different posts. The
one you're responding to was largely on-topic. The one I responded to
wasn't. Peter has a tendency to wander off into interminable, useless,
off-topic arguments, but he doesn't always do that. And in this he is
not alone.

[jillery]

On Thu, 11 Apr 2013 10:43:45 -0700, John Harshman

You continue to criticize me for doing that which you do yourself at
the same time. That's a very silly strategy.

Re-read his post. He specifically wrote "so I would like for us to
move this on-topic discussion to sci.bio.paleontology." That you
removed that newsgroup from the distribution list puts the lie to your
claim that nobody is moving anything.

>>>> Since the topic is "turtle genome sequence", the topic is explicitly
>>>> *not* "this thread has been pretty well hijacked in talk.origins by
>>>> people making personal attacks." So how you can say his comments
>>>> above are on-topic is beyond me.
>>>
>>> I was referring to the on-topic comments that were also in the post.
>>
>> In your post to which I replied, you make no such reference.
>
>Didn't think an explicit reference was necessary, since you were
>presumably capable of reading the parts of Peters post you deleted.

The parts I deleted were not relevant to my point. You replied to my
post, not his. There was nothing of his post relevant to the topic in
my post. Your self-justifying illogic knows no bounds.

>>>> You made substantially the same point here:
>>>>
>>>> <rNKdnSEEZLS...@giganews.com>
>>>>
>>>> so why you challenge me about it makes no sense. It's as if you think
>>>> only you have the authority to criticize him.
>>>
>>> No authority is needed. But in fact most of his post was on-topic.
>>
>> So you contradict yourself. No surprise there.
>
>You have an odd tendency to find what isn't there. Different posts.

You have an odd tendency to ignore what is directly in front of you.
Different posts, same problem.

>The
>one you're responding to was largely on-topic.

Perhaps for variations of "largely" devoid of meaning.

>The one I responded to
>wasn't. Peter has a tendency to wander off into interminable, useless,
>off-topic arguments, but he doesn't always do that. And in this he is
>not alone.

Yeppers, you share that trait with him.

[Richard Norman]

On Thu, 11 Apr 2013 02:03:13 -0400, jillery <69jp...@gmail.com>
wrote:

Sorry for the delay but I have had some other business to attend to.

I am not sure what you mean by "revert to the primitive form". The
paper discusses a number of specialized turtle features, especially
longevity, resistance to anoxia resistance to cold, tooth loss, and
temperature determination of sex but I don't think any of these are
primitive. They also describe a rather slow mutation rate in turtles
compared with other amniotes so, if anything, there is "retention of
primitive form" rather than "reversion".

I recall turtles being a real problem for a very long time now.
Fortunately I never had to teach details of vertebrate evolution. For
intro biology it was enough to get across the notion of how different
amniote development was from fish-amphibian and how placental
development was just a slight modification of the general amniote egg.
There was a total of two hours (OK, 2 * 50 minutes) for this whole
business -- one on amniotes and one on special adaptations of birds
and mammals. So you just omit all the gory details -- just blindly
proceed ahead and, if one or two rare students ask questions about it
then you can discuss it privately. Just explaining why "reptiles" no
longer exist was a mess and the bird-dinosaur business just took three
words to describe: "Birds are dinosaurs. Next question?"

[John Harshman]

On 4/11/13 3:38 PM, Richard Norman wrote:
> On Thu, 11 Apr 2013 02:03:13 -0400, jillery<69jp...@gmail.com>
> wrote:
>
>> On Wed, 10 Apr 2013 19:16:58 -0700, Richard Norman
>> <r_s_n...@comcast.net> wrote:
>>
>> [...]
>>
>>> So where do you stand on the group once called "Anapsida"? Do holes
>>> in the skull count for anything anymore?
>>
>>
>> I am no expert, but an interested observer, apparently like you. I
>> understand that in the past they had to rely on morphological
>> differences. It's reasonable to expect temporal fenestrae to be a
>> reliable indicator of lineage.
>>
>> But I also recognize that morphological interpretation can be
>> subjective and not detailed enough to distinguish many cases. All
>> other things being equal, I would bet on the genetic data. So a
>> question in my mind is what evolutionary process drove turtles to
>> revert to the primitive form? Perhaps it had something to do with the
>> development of their shells, but that's just speculation.
>
> Sorry for the delay but I have had some other business to attend to.
>
> I am not sure what you mean by "revert to the primitive form".

I think she's talking about the amniote skull. Ancestral amniotes had no
temporal fenestrae, ancestral diapsids had two, and turtles are back to
none. Hey, you're the one who brought up holes in the head.

[Richard Norman]

Sorry, Jillery. Now I understand.

It is just that I never bothered with the anatomy -- the physiology
was my thing and turtles had enough of that. The turtle heart is a
well known feature: it takes a licking and keeps on ticking. The
isolated heart will continue to beat for well over a day if you take
any reasonable care with it.

[jillery]

On Thu, 11 Apr 2013 16:29:04 -0700, Richard Norman

IIUC my use of the term is standard terminology, I will explain, just
in case anybody else claims confusion.

"Primitive" in this context does not mean less sophisticated, but less
derived, closer to the basal form. For this topic, the basal form is
a solid skull, in contrast to a skull with temporal fenestrae.
The question of Anapsida paraphyly implies that species ancestral to
modern turtles were diapsids, and some turtle lineages lost their
temporal fenestrae over time. In its turn, that implication raises a
question; what evolutionary pressure caused these lineages to lose
what appears to be an advantageous adaptation?

The reasons for my question, and my question, are clear and obvious,
and my question is relevant to the topic.

[Ron O]

What do you mean that "should the mob continue the beat down?" What
just happened in this thread, the part that you are responding to?
Someone has a very skewed view of reality. Nyikos obviously goes out
of his way to make trouble for himself. What has he told you? Did he
do what he said that he would do after delivering the third
knockdown? What does he do above instead of inform me that he has
already delivered his third delusional knockdown? I admit that his
behavior is sad, but I have no control over it.

Nyikos has gotten a lot of people ticked off because he is low life
scum. No one can do anything to fix that. Lying to yourself about
the facts is stupid and dishonest. Really what kind of person would
bleat and threaten about his knockdowns for a year and a half and then
do what Nyikos has done? You know for a fact that Nyikos' bleating
and whining have have been lies for the past year and a half and you
just can't do anything about it. If Nyikos was at all realistic and
not delusional would his three knockdowns have been so pathetically
stupid? Wouldn't he have just been able to go through a years worth
of posts and find something that he could have knocked me down with
instead of what he came up with? This is the type of dishonest and
delusional person that you are trying to defend.

I can't do anything about it, you should know by now that I avoid
contact with Nyikos. I probably shouldn't have because, apparently,
others like yourself, have catered to the squeaky wheel when Nyikos
bleats to other posters. They have the impression that we are going
at it, when it is all just Nyikos. What has Nyikos done with respect
to me in the last year and a half? He gave up on what we were arguing
about and has just been a delusional jerk. He obviously gets himself
into his messes with me. Did you bother to check out how often I
respond to Nyikos? How could someone else be the problem when I
didn't post to Nyikos for three months between July and October.
Nyikos was bleating and whining about me during that period, but I
wasn't involved.

People do not like Nyikos for a very simple reason. If you can't see
that you are just lying to yourself. There is no doubt that Nyikos is
a liar and he is delusional. The combination ticks a lot of people
off because Nyikos has enough on the ball to understand how badly off
he is, and he has a sadistic nature. I do not understand projection,
but Nyikos is in the delusional phase of the problem. He has
apparently created a fantasy world where he can never lose an
argument, and can never lie or do dishonest and bogus things. This is
a loser that claims that he has never lied on the internet, when lying
is a way of life for Nyikos.

You are defending a delusional loon that is responsible for the post
that I requote below. With this type of delusional attitude and
Nyikos' sadistic nature there will always be a problem. You may think
that sadistic is over the top, but Nyikos in his own projection put
the charge forward after starting a side thread to hurt and make fun
of someone else. It wasn't my problem when it turned out that Nyikos
had just made up the story. I didn't even know what was so funny, but
it was apparent that Nyikos was taking great glee and spreading what
he thought was torture over multiple posts before providing his bogus
punchline. When it all blew up in his face did he apologize? There
is no doubt that Nyikos understands that he does the things that he
does in order to hurt another person. His delusions and sadistic
nature tick people off.

QUOTE:
The relationship between me and the other talk.origins regulars wrt
accusations of malicious lies here is a lot like the relationship
between Bilbo and Gollum wrt riddles.

If I win, they lead me out of *one* cavern of back-and-forth with them
by ignoring the post where I do it.

If I lose, everyone who has ever decided to become an adversary of
mine gets to join in "devouring" my existence on Usenet.

Fortunately, I have never lost, and if I remain true to my nature, I
never will.

Bill got a little taste of why that is so, and even that little taste
seems to have led me out of the cavern of back-and-forth with him, at
least where this thread is concerned.

Peter Nyikos
END QUOTE:

http://groups.google.com/group/talk.origins/msg/c1c9a7bd4d8901b3?hl=en

Delusional and malicious, I rest my case.

Ron Okimoto

[John Harshman]

No, that's polyphyly. Anapsida is guaranteed to be paraphyletic as long
as it's defined by a primitive condition, regardless of turtle
relationships.

> In its turn, that implication raises a
> question; what evolutionary pressure caused these lineages to lose
> what appears to be an advantageous adaptation?

I don't know. But it's related to the question of why we have temporal
fenestrae in the first place. Lightening the skull? Better distribution
of stress? More room for jaw muscle attachment? More room for jaw
muscles to bulge out? Turtles have another strategy for the last two:
excavating the rear of the skull.

> The reasons for my question, and my question, are clear and obvious,
> and my question is relevant to the topic.

It is indeed.

[Richard Norman]

On Fri, 12 Apr 2013 04:11:47 -0400, jillery <69jp...@gmail.com>

Your question may have been clear and obvious to most but I missed it
so I asked what you meant. John gave a simple and clear explanation,
one which I should have understood, so I apologized. And yes, all this
is smack on topic. If anyone else is lurking, here is a page about
holes in the head, stuff that I really did once know but apparently
forgot:
http://tolweb.org/notes/?note_id=463

[Mark Isaak]

On 4/12/13 5:29 AM, Ron O wrote:
> [...]

Prepare yourself for a little more defense of a delusional loon.

> Nyikos obviously goes out of his way to make trouble for himself.

That is rather like saying, "Someone with Tourette's Syndrome goes out
of his way to display vocal tics."

> [...] There is no doubt that Nyikos is a liar and he is delusional.

I, for one, doubt that. "Lying", to me, means saying something that one
knows is false. Thus "lying to himself" does not really qualify as
lying. That is why, when die-hard creationists say something
egregiously wrong, I do not say they are lying, I say they are bearing
false witness. "Dishonest" is also often applicable when it is not a
one-time mistake. But "lying" includes moral implications that I do not
recall seeing in Nyikos. (But then, I have seen none of his posts for
the last month or so.) And if you want to highlight his immoral
behaviors, it's not like you have that much further to look.

> You are defending a delusional loon that is responsible for the post
> that I requote below. With this type of delusional attitude and
> Nyikos' sadistic nature there will always be a problem. You may think
> that sadistic is over the top, but Nyikos in his own projection put
> the charge forward after starting a side thread to hurt and make fun
> of someone else. It wasn't my problem when it turned out that Nyikos
> had just made up the story. I didn't even know what was so funny, but
> it was apparent that Nyikos was taking great glee and spreading what
> he thought was torture over multiple posts before providing his bogus
> punchline. When it all blew up in his face did he apologize? There
> is no doubt that Nyikos understands that he does the things that he
> does in order to hurt another person. His delusions and sadistic
> nature tick people off.
>

> [snip requote]

And that I agree with 100%. The really pathetic part is that, to all
appearances, when he hurts someone else, he considers himself to be
"winning."

--
Mark Isaak eciton (at) curioustaxonomy (dot) net
"It is certain, from experience, that the smallest grain of natural
honesty and benevolence has more effect on men's conduct, than the most
pompous views suggested by theological theories and systems." - D. Hume

[Ron O]

On Apr 12, 2:19�pm, Mark Isaak <eci...@curioustax.onomy.net> wrote:
> On 4/12/13 5:29 AM, Ron O wrote:
> �> [...]
>
> Prepare yourself for a little more defense of a delusional loon.
>
> > Nyikos obviously goes out of his way to make trouble for himself.
>
> That is rather like saying, "Someone with Tourette's Syndrome goes out
> of his way to display vocal tics."

Why do you think that I don't go out of my way to provoke the loon?
This does seem to have its down side, because if you read responses to
me by guys like Norman and Burkhard you get the impression that
Nyikos' big lie strategy works on some people that don't bother to
look into the facts.

In the same thread that the quoted part below comes from Gans mentions
that in his experience that not defending yourself leaves you open to
people believing the liar. I don't read much of what Nyiikos posts,
but from the little that I read, I know that he has a pretty incessant
whine with reguards to me. Apparently guys like Norman and Burkhard
don't find anything strange about the Nyikosian whine even when I
haven't posted to the boob for weeks or months. So there is an
apparent downside to not responding the the boob.

>
> > [...] �There is no doubt that Nyikos is a liar and he is delusional.
>
> I, for one, doubt that. �"Lying", to me, means saying something that one
> knows is false. �Thus "lying to himself" does not really qualify as
> lying. �That is why, when die-hard creationists say something
> egregiously wrong, I do not say they are lying, I say they are bearing
> false witness. �"Dishonest" is also often applicable when it is not a
> one-time mistake. �But "lying" includes moral implications that I do not
> recall seeing in Nyikos. �(But then, I have seen none of his posts for
> the last month or so.) �And if you want to highlight his immoral
> behaviors, it's not like you have that much further to look.

Immoral behaviors? Do you count dishonest discourse in order to
mislead from or counter a point by misstating the facts as being
immoral? Nyikos does that all the time. He understands that he does
it because he has a rule about why he can get away with doing it. He
believes that if he removes the evidence that he is lying from a post,
even if you can just go up one post to see what he deleted (without
attribution most of the time), that he isn't lying because the
evidence does not exist in the post that he is telling the lie in. He
will delete the same material and tell the same lie again if it is
requoted. He usually runs and doesn't do it a third time because he
has some weird rule about doing something bogus and dishonest three
times. Has Nyikos ever told you about his evidence in one post rule
about lying? There is no doubt that Nyikos does the dishonest
deletion on purpose (Who projected his foibles in the thread on
dishonest deletia that he recently started?). He is very assiduous
about removing the evidence before lying. He even bragged about never
having the evidence that he lies in one post. That is just his most
obvious immoral behavior.

What about his stupid lies that he has to tell in order to maintain
his lunatic notion that he has never lost an argument on the
internet? Those lies are often the stupidest and often laced with
malicious personal attacks.

>
> > You are defending a delusional loon that is responsible for the post
> > that I requote below. �With this type of delusional attitude and
> > Nyikos' sadistic nature there will always be a problem. �You may think
> > that sadistic is over the top, but Nyikos in his own projection put
> > the charge forward after starting a side thread to hurt and make fun
> > of someone else. �It wasn't my problem when it turned out that Nyikos
> > had just made up the story. �I didn't even know what was so funny, but
> > it was apparent that Nyikos was taking great glee and spreading what
> > he thought was torture over multiple posts before providing his bogus
> > punchline. �When it all blew up in his face did he apologize? �There
> > is no doubt that Nyikos understands that he does the things that he
> > does in order to hurt another person. �His delusions and sadistic
> > nature tick people off.
>
> > [snip requote]
>
> And that I agree with 100%. �The really pathetic part is that, to all
> appearances, when he hurts someone else, he considers himself to be
> "winning."

When he hurts someone with his lies is that being immoral enough to be
a liar? Anyone can be wrong, but Nyikos will remove the evidence and
lie in order to do something dishonest, and he will often add his
weird projective personal attacks about things ranging from family
abuse to nervous breakdowns when he is doing it. I think Nyikos
qualifies as a liar by any standards except his own.

Ron Okimoto

[John Harshman]

On 4/12/13 4:13 PM, Ron O wrote:
> On Apr 12, 2:19 pm, Mark Isaak<eci...@curioustax.onomy.net> wrote:
>> On 4/12/13 5:29 AM, Ron O wrote:
>> > [...]
>>
>> Prepare yourself for a little more defense of a delusional loon.
>>
>>> Nyikos obviously goes out of his way to make trouble for himself.
>>
>> That is rather like saying, "Someone with Tourette's Syndrome goes out
>> of his way to display vocal tics."
>
> Why do you think that I don't go out of my way to provoke the loon?

But you do. His first post in this thread was a perfectly reasonable
series of on-topic statements, and your response was a way over-the-top
rant.

[Ron O]

With our history is anything perfectly reasonable with Nyikos? Why
lie to yourself like this? Do you think that Nyikos was trying to be
nice? Pretending doesn't change anything. Why didn't he inform me
that he had supposedly delivered his third knockdown several weeks ago
when he had the chance. This isn't the first post to me since he
supposedly was going to stop posting to me. What was he going to do
months from now?

Is he still claiming that you are a liar and that he is kicking your
butt around TO? You know what he is like, why even try to defend the
guy. I'm the one that doesn't want Nyikos posting to me. You are the
one that seems to like the attention and don't mind taking advantage
of the incompetent boob. Nyikos may not be able to help himself, but
that doesn't mean that people have to make it easy for him or
encourage him to be such an ass.

Ron Okimoto

[Mark Isaak]

On 4/12/13 4:13 PM, Ron O wrote:

> On Apr 12, 2:19 pm, Mark Isaak <eci...@curioustax.onomy.net> wrote:
>> On 4/12/13 5:29 AM, Ron O wrote:
>> > [...]
>>
>> Prepare yourself for a little more defense of a delusional loon.
>>
>>> Nyikos obviously goes out of his way to make trouble for himself.
>>
>> That is rather like saying, "Someone with Tourette's Syndrome goes out
>> of his way to display vocal tics."
>
> Why do you think that I don't go out of my way to provoke the loon?

Read again. It is Nyikos, not you, whom I was talking about.

> In the same thread that the quoted part below comes from Gans mentions
> that in his experience that not defending yourself leaves you open to
> people believing the liar. I don't read much of what Nyiikos posts,
> but from the little that I read, I know that he has a pretty incessant
> whine with reguards to me. Apparently guys like Norman and Burkhard
> don't find anything strange about the Nyikosian whine even when I
> haven't posted to the boob for weeks or months. So there is an
> apparent downside to not responding the the boob.

Nyikos whines about lots of people. In doing so, he tells all but the
most socially illiterate readers a lot about himself and little or
nothing about whom he is whining about.

All of that looks to me like delusion, not lying.

>>> You are defending a delusional loon that is responsible for the post
>>> that I requote below. With this type of delusional attitude and
>>> Nyikos' sadistic nature there will always be a problem. You may think
>>> that sadistic is over the top, but Nyikos in his own projection put
>>> the charge forward after starting a side thread to hurt and make fun
>>> of someone else. It wasn't my problem when it turned out that Nyikos
>>> had just made up the story. I didn't even know what was so funny, but
>>> it was apparent that Nyikos was taking great glee and spreading what
>>> he thought was torture over multiple posts before providing his bogus
>>> punchline. When it all blew up in his face did he apologize? There
>>> is no doubt that Nyikos understands that he does the things that he
>>> does in order to hurt another person. His delusions and sadistic
>>> nature tick people off.
>>
>>> [snip requote]
>>
>> And that I agree with 100%. The really pathetic part is that, to all
>> appearances, when he hurts someone else, he considers himself to be
>> "winning."
>
> When he hurts someone with his lies is that being immoral enough to be
> a liar?

No. Lying implies immorality (and even that has exceptions), but
immorality does not imply lying. Note, for example, that there are
traditionally seven deadly sins, and lying is not among them.

[Paul J Gans]

John, that's because THERE IS NO FIRST POST. Peter will frequently
refer to posts made in the mid 1990's, especially to attack people.
Simply changing the header does not really mean that a new
argument has started. Consider the posts on panspermia. Those
threads are almost TWENTY YEARS OLD.

--
--- Paul J. Gans

[pnyikos]

On Apr 10, 6:51�ｿｽpm, John Harshman <jharsh...@pacbell.net> wrote:
> On 4/10/13 3:30 PM, pnyikos wrote:
> > On Apr 10, 5:46 pm, John Harshman<jharsh...@pacbell.net> �ｿｽwrote:

> >> On 4/10/13 2:34 PM, alias Ernest Major wrote:
>
> >>> On 10/04/2013 21:56, Richard Norman wrote:
>
> >>>> I would prefer to return to the topic and so I ask John why
> >>>> "traditional systematists" are held in such low regard. Isn't this
> >>>> just a typical arrogance of the molecular people when there is
> >>>> disagreement about lineage? Is there a consensus about turtles or is
> >>>> there really some debate?
>
> >>> I think you'll find that it's not morphological vs molecular, but
> >>> traditional vs cladistic. (I'm all that sure of the low regard either.)
>
> > I think it is molecular vs. morphological that takes into account
> > extinct taxa, like *Eusthenopteron*.
>

> Then you are wrong. I think you're confusing the discussion of turtle
> cladistic relationships (not traditional systematics) with your ideas of
> close relationships to ancestors (traditional).

You misunderstood my intent, and maybe I misunderstood Ernest Major's
intent. I was thinking of the last question Richard Norman asked, as
to wheret the controversy about turtle ancestry is centered.

A number of months ago I read an article by Gauthier in which he
described his latest morphological cladistic analysis, in which
extinct as well as extant species were incuded. Among them was the
enigmatic *Eunotosaurus* as well as the earliest known Chelonian. And
the result was that turtles were classed as anapsids.

> >>> The problem with traditional systematics is baseing classifications on a
> >>> small number of subjectively selected "key" characters, rather than on
> >>> all the evidence.
>
> > Largely true, but subjectivity is in the eye of the beholder.
>
> > For instance, I've said in the past that just the structure of the
> > shoulder girdle in the monotremes vs. marsupials and placentals should
> > outweigh a really hefty number of minor (especially molecular)
> > characters as far as what is the sister group of what.
>
> > The scapula of marsupials and placentals is essentially identical,
> > even to a raised median ridge, while that of monotremes is utterly
> > different.

And harking back to therapsids and even pelycosaurs. There is a
series of fine drawings in Romer's _Vertebrate Paleontology showing
shoulder girdles of *Ophiacodon* (a pelycosaur), *Kannemeyeria* (a
dicynodont), the platypus, and the Virginia opossum. The first three
resemble each other far more than the last two resemble each other,
even when the extra elements of the first three shoulder girdles are
disregarded.

> >�ｿｽAlso there is at least one extra element in the monotreme
> > shoulder girdle.

Two. The interclavicle and the procoracoid.

> > Harshman's reply was a dismissive "If only it were that simple". �ｿｽHad

> > I said "all" except "a really hefty" [actually, words to that effect]

> > he would have been on target. �ｿｽInstead I think it would have been more

> > appropriate for him to say "I'm glad the process we use is not so
> > complicated."
>

> We'll all do better if you stop these retrospective judgments rendered
> to third parties.

You have complete freedom to update your opinion, but you do not avail
yourself of it.

> >> That wasn't quite the "traditional" that Peter was talking about. He was
> >> referring, essentially, to gradism.
>
> > If you are referring to grades as in "subholostean grade" and

> > "holostean grade" you are dead wrong. �ｿｽThat is the only example of

> > polyphyletic taxon that Romer gave in _Vertebrate Paleontology_, the
> > example of both the bowfin and the gar being in Holostei.

No reply to this from you, so I am still confused by what you mean by
"gradism." For now I will assume you really meant to refer to what I
described next:

> > What I keep referring to is the traditional Linnean classification
> > whereby every organism had its own genus, family, order etc.
> > [including some intermediates like "suborder," "infraorder,"

> > "superfamily" in some cases]. �ｿｽCladistic classification is great for

> > extant taxa, but the further back in time one goes, the more
> > unsatisfactory it is.
>

> You have confused cladistic classification with unranked classification.
> It's possible to have a cladistic, Linnean classification.

For extant animals, it is. But for extinct species it gets worse and
worse the further back one goes. Organisms are all put at leaves due
to the taboo against depicting them in the position of ancestors. As
a result, stem species could have nothing besides a gigantic clade to
put them in, perhaps one containing the whole of tetrapoda, without
any family or even class to belong to.

In the traditional classification, these are in the paraphyletic class
Amphibia, and whether they are in a family or order all by themselves
is determined by how different they are from the nearest species in
morphology.

> And of course
> you like the traditional classification because it's all about grades.

And all the advantages they provide. And you like the cladistic
because it is willing to pay any price for "objectivity," even at the
cost of being unable to orient oneself without putting untold hours
into studying minutiae.

> > In guides to mushrooms, trees, etc. one has means of identification
> > for non-specialists that classifies things according to spore print

> > and other visible characters. �ｿｽIf a fossil has the various apomorpies

> > that narrow down its clade missing, at least the Linnean
> > classification gave other ready criteria for identifying it, or at
> > least narrowing it down to the smallest feasible Linnean taxon.
>

> Not really, no.

You have a knack for bland denials. I hope what I say next won't get
the same bland treatment.

Scene: a fossil hunter finds a scapula prartly buried in the ground
and asks an expert anatomist what he makes of it.

"Without removing more of the surrounding matrix, I can't say very
much except that it is a tetrapod, but neither a bird nor a marsupial
nor a placental. Do you know the age of this outcrop?"

"No, it's different from the ones we've identified so far, and the
geologist who could answer that question is already on his way home."

But after the better part of an hour, the fossil hunter uncovers
another bone from the skeleton and calls it to the attention of the
anatomist.

"That settles it!" the anatomist cries. "It's a mammal, perhaps a
monotreme. You've got a very significant find here, perhaps shedding
a lot of light on mammalian relationships. In the few days left to us
before we head for home, we should make every effort to unearth this
entire fossil to take with us. A find like this comes along only a
few times in a lifetime."

Concluded in next reply.

Peter Nyikos

[John Harshman]

That's the sort of outburst that shows you have become seriously
irrational where Peter is concerned.

[John Harshman]

Go back and read Peter's actual first post in this thread. Nothing of
the sort you are talking about is there.

[Ron O]

On Apr 12, 7:57�pm, Mark Isaak <eci...@curioustax.onomy.net> wrote:
> On 4/12/13 4:13 PM, Ron O wrote:
>
> > On Apr 12, 2:19 pm, Mark Isaak <eci...@curioustax.onomy.net> wrote:
> >> On 4/12/13 5:29 AM, Ron O wrote:
> >> � > [...]
>
> >> Prepare yourself for a little more defense of a delusional loon.
>
> >>> Nyikos obviously goes out of his way to make trouble for himself.
>
> >> That is rather like saying, "Someone with Tourette's Syndrome goes out
> >> of his way to display vocal tics."
>
> > Why do you think that I don't go out of my way to provoke the loon?
>
> Read again. �It is Nyikos, not you, whom I was talking about.
>
> > In the same thread that the quoted part below comes from Gans mentions
> > that in his experience that not defending yourself leaves you open to
> > people believing the liar. �I don't read much of what Nyiikos posts,
> > but from the little that I read, I know that he has a pretty incessant
> > whine with reguards to me. �Apparently guys like Norman and Burkhard
> > don't find anything strange about the Nyikosian whine even when I
> > haven't posted to the boob for weeks or months. �So there is an
> > apparent downside to not responding the the boob.
>
> Nyikos whines about lots of people. �In doing so, he tells all but the
> most socially illiterate readers a lot about himself and little or
> nothing about whom he is whining about.

It has become my experience that this is not the case for all people
who want to comment on the situation when they are obviously ignorant
of the situation, or have reasons of their own for encouraging the
boob.

Nyikos obviously lies to maintain his delusions. I do not deny that.
He does so in a malicious way. He understands what he is doing
because you just have to see what he claims about others who are
supposedly doing what he knows that he is doing. If he didn't know he
what he was doing would he project his bogus behavior onto others?
Would he have his stupid one post lie rule or his limit of doing the
same bogus and dishonest thing more than twice if he didn't understand
what he was doing? Yes he does these things and has these rules to
support his delusions, but it shows that he has enough on the ball to
understand what he is doing, and that he needs these rules to keep
doing the junk.

>
> >>> You are defending a delusional loon that is responsible for the post
> >>> that I requote below. �With this type of delusional attitude and
> >>> Nyikos' sadistic nature there will always be a problem. �You may think
> >>> that sadistic is over the top, but Nyikos in his own projection put
> >>> the charge forward after starting a side thread to hurt and make fun
> >>> of someone else. �It wasn't my problem when it turned out that Nyikos
> >>> had just made up the story. �I didn't even know what was so funny, but
> >>> it was apparent that Nyikos was taking great glee and spreading what
> >>> he thought was torture over multiple posts before providing his bogus
> >>> punchline. �When it all blew up in his face did he apologize? �There
> >>> is no doubt that Nyikos understands that he does the things that he
> >>> does in order to hurt another person. �His delusions and sadistic
> >>> nature tick people off.
>
> >>> [snip requote]
>
> >> And that I agree with 100%. �The really pathetic part is that, to all
> >> appearances, when he hurts someone else, he considers himself to be
> >> "winning."
>
> > When he hurts someone with his lies is that being immoral enough to be
> > a liar?
>
> No. �Lying implies immorality (and even that has exceptions), but
> immorality does not imply lying. �Note, for example, that there are
> traditionally seven deadly sins, and lying is not among them.

Nyikos doesn't tell the truth. He does it to prevaricate about
reality, and to hurt other people. There is no doubt that, at times,
Nyikos makes up his stories in order to hurt others. You just have to
go to the obvious example where he started a side thread complete with
stupid title change to make fun of me. He drew the topic out over
several posts obviously taking great glee in doing what he thought
that he was doing. He took the time to give a lecture while claiming
that someone else had done something really funny. When the punchline
came it was just a made up story that could have never happened
because Google doesn't work that way. When Nyikos realized that
reality didn't support his claims he projected his own intent onto his
victim and claimed that his victim was the sadist. He knew what he
had just tried to do. He had initiated a thread title change in order
to do it. His delusion became apparent, but his intent was sadistic,
by his own admission via his normal behavior of projecting his
stupidity onto others. Nyikos understood that he was trying to hurt
someone else. The way that he defends such behavior is to claim that
someone else is doing it.

I do not contest that his delusions got him into trouble, but he
obviously had malicious intent and was willing to lie in order to do
what he wanted to do. I don't consider it a deadly sin, but it is
malicious asinine behavior, and it is irritating. The example above
is not an isolated event. There are multiple threads that I can point
to with Nyikos doing essentially the same thing except he started
whole threads to do it, and not just with respect to me. The insanity
defense doesn't work if the defendant has enough on the ball to
understand that what he is doing is wrong. Nyikos knows that it is
wrong. In his own projection he tells everyone just how wrong he
thinks that it is.

Ron Okimoto

[Richard Norman]

You seem fixated on some particular morphological features and the
opinions of some particular systemacists ignoring the fact that there
has been enormous controversy over just how to place turtles with an
enormity of disagreement. Romer's book, of course, is now almost 50
years old. Paleontologists, of course, generally have only morphology
of fossils to go on but that is not the be-all and end-all of
evolutionary information.

In particular, the post that started this thread cited an analysis of
the genome of a turtle. That paper concluded through a number of
independent lines of genetic information that turtles agreed more
closely with crocodilians and birds than with snakes and lizards. That
is not a pattern that you would expect for the anapsida.

[pnyikos]

On Apr 10, 6:51�pm, John Harshman <jharsh...@pacbell.net> wrote:
> On 4/10/13 3:30 PM, pnyikos wrote:

> > On Apr 10, 5:46 pm, John Harshman<jharsh...@pacbell.net> �wrote:
> >>> How to weight
> >>> traits is a difficult question to answer, but weighting them all the
> >>> same is clearly at best a simplifying approximation.
>
> > At worst, it is pseudoscience.
>
> Why?

Because you might be giving as much weight to twenty, or whatever,
base pairs as you do to all the differences you have formally
described in the monotreme and placental-marsupial scapulas. Or to a
hundred base pairs as to all the similarities you see in the wings of
megabats and microbats.

And, as you know, although all base pairs are equal, some are far more
equal than others, resulting in huge differences in anatomy and mode
of life.

> >>> And selecting the
> >>> traits to use in an analysis remains a subjective process, leading
> >>> cherry picking still being a hazard.
>
> > I confine myself to clear cut cases like the two I've given above and
> > in the past.
>
> If only it were that simple, to coin a phrase.

It is that simple, because I am not a professional and do not have to
bother with cases that are not so clear cut. But I will insist that
"extraordinary claims require extraordinary evidence" to anyone who
claims the two kinds of bats evolved flight independently, or that
monotremes form a clade with placentals that excludes marsupials.

Peter Nyikos

[pnyikos]

On Apr 10, 7:47�pm, Richard Norman <r_s_nor...@comcast.net> wrote:

> On Wed, 10 Apr 2013 15:30:30 -0700 (PDT), pnyikos
> <nyik...@bellsouth.net> wrote:
> >On Apr 10, 5:46�pm, John Harshman <jharsh...@pacbell.net> wrote:

> >> On 4/10/13 2:34 PM, alias Ernest Major wrote:

> >> > And on the other hand one can criticise equal weighted maximum parsimony
> >> > as a technique - it leads to papers claiming that flight (re-)evolved n
> >> > times in stick insects, rather than being lost n+1 times.
>
> >I'm unfamilar with that example, but see above about radically
> >different weightings. �Another example is megabats v. microbats. �A
> >look at how the two inner digits of the wings are close together in
> >both, as well as the whole overall shape of the wings, should have
> >made everyone treat the hypothesis that they evolved flight separately
> >with the formula, "Extraordinary claims require extraordinary
> >evidence."
>
> >Ditto the claim that marsupials are sister group to
> >{placentals ,monotremes}.

[snip]

> >> > And selecting the
> >> > traits to use in an analysis remains a subjective process, leading
> >> > cherry picking still being a hazard.
>
> >I confine myself to clear cut cases like the two I've given above and
> >in the past.

Here is the monotreme placement case, with some additional comments I
made to John a bit earlier this evening.

> > For instance, I've said in the past that just the structure of the
> > shoulder girdle in the monotremes vs. marsupials and placentals should
> > outweigh a really hefty number of minor (especially molecular)
> > characters as far as what is the sister group of what.
>
> > The scapula of marsupials and placentals is essentially identical,
> > even to a raised median ridge, while that of monotremes is utterly
> > different.

And harking back to therapsids and even pelycosaurs. There is a
series of fine drawings in Romer's _Vertebrate Paleontology showing
shoulder girdles of *Ophiacodon* (a pelycosaur), *Kannemeyeria* (a
dicynodont), the platypus, and the Virginia opossum. The first three

resemble each other far, far more than the last two resemble each

other, even when the extra elements of the first three shoulder
girdles are disregarded.

> > Also there is at least one extra element in the monotreme
> > shoulder girdle.

Two. The interclavicle and the procoracoid.

> I do not understand why your selection of morphologial �characters
> should have more weight than somebody elses. �You say you have reasons
> but then so does everybody else. �In other words, it really isn't that
> simple.

Take a look at a good reproduction of just the scapulas alone, and
you should be struck by the difference. How can even a hundred base
pairs compete with that?

If you can't find any, I'm sure you can find detailed pictures of
megabat and microbat wings, and see how the claim that they
independently evolved from non-flying mammals was truly an
extraordinary one.

> You may confine yourself to clear cut cases (whether the two you gave
> are such is another problem) but isn't that a form of cherry picking?
> You simply abandon anything tricky?

I abandon it to the cladists, who have the tools to make distinctions
where there are no well-established key characters that we can treat
the way Supreme Court justices described pornography, "We know it when
we see it."


> And "traditional" classification is more than Linnean categories. � I
> think a good example of grades is given by the quite traditional
> notion of acoelomate, pseudocoelomate, and coelomate kinds of
> protostome. �Or non-vascular vs. vascular plants.

Don't the vascular ones form a clade? In that case, the non-vascular
ones are a paraphyletic group. Perhaps they are too big a hunk of
Plantae to comfortably fit into the limited number of Linnean grades,
but the classification has tolerated ungraded categories in the past.


> �But then I am not a
> systemacist so I am not in a position to say what specialists in this
> area consider "traditional" just as I am not in a position to evaluate
> why this particular feature should count with heavier weight than that
> one. �I do know that counting as separate features those that are
> really highly correlated by one developmental process is flawed.

Yes, that's another reason I say that weighting characters equally is
"at worst" pseudoscience.

Peter Nyikos

[Robert Camp]

No one is making it easy for him and no one is encouraging him to be
an ass. Almost everyone responding to you in this thread has suffered
the brunt of Peter's afflictions. But the point is that this isn't
about Nyikos. It's about encouraging you to avoid emulating his
behavior. You can't control what he says and does, you're not going to
change him regardless of how you respond to him. So losing perspective
over this thing can only hurt you.

When you say he's a conniving lying scoundrel, or a scumbag, or
mentally incompetent, it seems pretty clear to me that you're no
longer thinking about this rationally. He's volatile, no doubt, but I
think scoundrel and scumbag are way over the top. And he's not
mentally incompetent, he's very capable of maintaining a substantive
discussion. He's a smart, educated guy who's got some socialization
problems.

If he really is aware of his own transgressions then it seems likely
he's looking for attention, and in that case the best thing to do is
deny him that. But if, as I believe, he cannot help himself, then
squabbling with him is not only undesirable, it's unkind. In either
case it seems to me you benefit by just letting things drop.

[Richard Norman]

The enormity of the genetic data, far more than a few hundred
nucleotides, and the immediacy of the genetic data to the theoretical
foundations of evolutionary theory as opposed to the morphological
data being far down the line of phenotypic development gives
importance to the "new" thinking. There are a very large number of
cases where the genetic data has completely reorganized thinking about
evolutionary patterns that had been established for decades. The
"protostomes" have gone through massive revisions most recently just a
couple decades ago.

If you cherry pick the examples you are willing to discuss no doubt
you can find beautiful examples of particular morphological features
that "prove" your point. However if the genomic data contradicts
that, then which is to be believed? There are cases where all these
problems remain to be sorted out but I think a smart move is to put
your money on the molecular data.

[pnyikos]

On Apr 12, 9:08�pm, Paul J Gans <gan...@panix.com> wrote:

OK, this is on topic for talk.origins even though it is new to this
thread.

> �Consider the posts on panspermia. �Those

> threads are almost TWENTY YEARS OLD.

There have been lots of threads on that theory, none lasting more than
a few months. The above is like saying "those threads about
Intelligent Design are almost TWENTY YEARS OLD" when referring to all
the threads that started out devoted to that particular topic.

I've even started threads that are not about directed panspermia *per
se* but about abiogenesis (including two about the protein takeover);
about the various stages in the evolution of life; and about modes of
space travel. But they are crucial to the whole theory, which brings
together a lot of seemingly unrelated themes.

Here's a different kind of example: Marc Tessera took a thread that
started out talking about something rotten in talk.origins and, with
my cooperation, has now metamorphosed it into one on terrestrial vs.
extraterrestrial origin of earth life -- discussion of directed
panspermia by another name.

Peter Nyikos

[Ron O]

Irrational? Do you contest the facts? I think that you are the one
that is being defensive because you are the one that seems to like
interacting with Nyikos in spite of the facts. Do I pester you about
your behavior with regards to Nyikos? What was your comment to me
when you were posting more than an order of magnitude more posts to
Nyikos than I was? I think that you are the one that needs to figure
out why you post to Nyikos so much. It has to be irritating because I
get the spill over of Nyikos whining about you in his posts to me.
Senseless crap about what a liar you are and how he is beating you
down, when I can have no opinion on the matter because I don't know
what he is talking about. What is so wrong about not wanting to
interact with Nyikos when he is exactly what I claim? Nyikos'
delusions make him an easy target, and there is no doubt that he is a
Dunning-Kruger candidate when it comes to the estimate of his own
internet competence, but he isn't a happy drunk, and it isn't very
pleasant when he finds out that he is wrong about something. So look
in the mirror and see if you like what you see there. I just want
Nyikos to go away and leave me alone. Who wants him to stick around
as a sparring partner? What kind of sport is it?

Ron Okimoto

[pnyikos]

On Apr 12, 10:32�pm, Richard Norman <r_s_nor...@comcast.net> wrote:
> On Fri, 12 Apr 2013 18:58:39 -0700 (PDT), pnyikos

> <nyik...@bellsouth.net> wrote:

> >On Apr 10, 6:51�pm, John Harshman <jharsh...@pacbell.net> wrote:
> >> On 4/10/13 3:30 PM, pnyikos wrote:

> >> > On Apr 10, 5:46 pm, John Harshman<jharsh...@pacbell.net> �wrote:

> >> >> On 4/10/13 2:34 PM, alias Ernest Major wrote:
>
> >> >>> On 10/04/2013 21:56, Richard Norman wrote:
>
> >> >>>> I would prefer to return to the topic and so I ask John why
> >> >>>> "traditional systematists" are held in such low regard. Isn't this
> >> >>>> just a typical arrogance of the molecular people when there is
> >> >>>> disagreement about lineage? Is there a consensus about turtles or is
> >> >>>> there really some debate?
>
> >> >>> I think you'll find that it's not morphological vs molecular, but
> >> >>> traditional vs cladistic. (I'm all that sure of the low regard either.)
>
> >> > I think it is molecular vs. morphological that takes into account
> >> > extinct taxa, like

*Eunotosaurus*.

>
> >> Then you are wrong. I think you're confusing the discussion of turtle
> >> cladistic relationships (not traditional systematics) with your ideas of
> >> close relationships to ancestors (traditional).
>
> >You misunderstood my intent, and maybe I misunderstood Ernest Major's
> >intent. �I was thinking of the last question Richard Norman asked, as

> >to where the controversy about turtle ancestry is centered.

>
> >A number of months ago I read an article by Gauthier in which he
> >described his latest morphological cladistic analysis, in which
> >extinct as well as extant species were incuded. �Among them was the
> >enigmatic *Eunotosaurus* as well as the earliest known Chelonian. �And
> >the result was that turtles were classed as anapsids.

The above was followed (spatially, not chronologically) by a long
discussion on a completely different topic:

> >> >>> The problem with traditional systematics is baseing classifications on a
> >> >>> small number of subjectively selected "key" characters, rather than on
> >> >>> all the evidence.

[snip long discussion about that last sentence]

> You seem fixated on some particular morphological features and the
> opinions of some particular systemacists ignoring the fact that there
> has been enormous controversy over just how to place turtles with an
> enormity of disagreement.

The morphological features on which I was "fixated" had nothing to do
with turtles. Gauthier et.al. did not just focus on some particular
morphological features in that article to which I was referring. They
used a proper cladistic analysis.

I believe I was the first person in talk.origins to call attention to
this striking discrepancy between the placement of turtles by a
molecular study and their traditional classification as anapsids.

At the beginning of 1998, Laurence Moran posted about an article on
phylogeny as suggested by molecular analysis of alpha and beta
hemoglobin, and myoglobin. The authors briefly mentioned a feature
that they noticed was unusual: mammals being closer to birds than
either was to lizards and snakes.

However, they (and also Moran) had overlooked an anomaly I found
equally striking: turtles within archosauria, with birds being more
closely related (cladistically speaking) to them and to Sphenodon than
to crocodilians. Here is the post where I made a big fanfare out of
it--it seemed so radical at the time:

http://groups.google.com/group/talk.origins/msg/c98d0b20052ff803

And here is an excerpt from another post:

===================== begin excerpt

See the above paper, where the performance is mixed. Five incorrect
(IMO) groupings had bootstrap values over 50 for NJ. Removing the
viper led to a much more sensible arrangement--except that the
bootstrap NJ value for grouping non-lizards, including mammals,
away from lizards shot up to 80. With the viper included,
it was below 40. But then, how can you trust a system
which puts the viper as more closely related to horses and
humans than to ANY of the other reptiles, including lizards?

To be sure, the bootstrap values for putting the viper with
us were below 40%, but that was what was keeping
the bootstrap value for the {birds, crocodilians, mammals,
turtles, Spenondon} group away from lizards from shooting up to 80.

=========================== end of excerpt

>�Romer's book, of course, is now almost 50

> years old. �Paleontologists, of course, generally have only morphology
> of fossils to go on but that is not the be-all and end-all of
> evolutionary information.

I never said it was, and neither did Gauthier. Recall the words I
quoted to Harshman:

"At least two total evidence analyses (in which molecular and
morphological data are combined) suggest that turtles are not
diapsids
(Lee, 2001; Frost et al., 2006). In both, the molecular characters
are
much more numerous than the morphological ones, which implies
significant support for the placement of turtles outside diapsids in
these molecular datasets."

I can't see why Harshman had difficulty with this passage. To me it
seems perfectly straightforward: if the molecular evidence were
overwhelmingly in favor of turtles being diapsids then their sheer
number would have caused these two analyses to put turtles into
Diapsida. But in fact they did not do that, so the molecular evidence
would seem to be only slightly in favor of them being diapsids.

> In particular, the post that started this thread cited an analysis of
> the genome of a turtle. �That paper concluded through a number of
> independent lines of genetic information that turtles agreed more
> closely with crocodilians and birds than with snakes and lizards.

But there were also a number of lines where the outcome had them
outside the diapsid clade, or in a clade with snakes and lizards. If
you look at the diagrams in the huge linked pdf file, you will see
some of them.

> That
> is not a pattern that you would expect for the anapsida.

No, of course not.

Peter Nyikos

[Ron O]

Do you actually disagree that Nyikos is a conniving lying scoundrel (I
don't recall using thos exact words, but they fit). He is a scumbag.
The word assoholic was coined for someone like Nyikos. I "lost" my
perspective on Nyikos long ago. It hasn't changed with any of his
recent behavior.

What did he just do for his last knockdown? There is no doubt that
Nyikos is mentally incompetent. Just because he can carry on a normal
conversation once in a while doesn't mean that he isn't delusional.
That is mental incompetence.

QUOTE:
The relationship between me and the other talk.origins regulars wrt
accusations of malicious lies here is a lot like the relationship
between Bilbo and Gollum wrt riddles.

If I win, they lead me out of *one* cavern of back-and-forth with them
by ignoring the post where I do it.

If I lose, everyone who has ever decided to become an adversary of
mine gets to join in "devouring" my existence on Usenet.

Fortunately, I have never lost, and if I remain true to my nature, I
never will.

Bill got a little taste of why that is so, and even that little taste
seems to have led me out of the cavern of back-and-forth with him, at
least where this thread is concerned.

Peter Nyikos
END QUOTE:

http://groups.google.com/group/talk.origins/msg/c1c9a7bd4d8901b3?hl=en

You know Nyikos, what must have been his state of mind when he wrote
the above post? Was he mentally competent at the time?

Yes, I call him names. The names were invented for people like
Nyikos, and it took months of Nyikosian stupidity to get that far. I
am not lying about the guy. Telling the truth about him is the only
thing that makes him think twice. Nyikos knows it because he had to
claim that the truth was slander, and the truth was only bad because
Nyikos is so bad. He does do the stupid and dishonest junk or he
wouldn't have taken a year and a half to deliver his three
knockdowns. All he would have needed to do was demonstrate that I had
lied or made up some story about him. He was always the one making up
the stories, and he knew it with enough conviction to run from his
threats for a year and a half. If I had made one false claim about
Nyikos it all would have been different, but Nyikos literally could
not come up with a single thing that he could knock me down with.
Really, look at his first two knockdown attempts. I can supply the
posts if you don't recall them. How sad and dishonest were they?
Basically all Nyikos has been doing with respect to me for the last
year and a half is lying about lying. That is what I have had to deal
with and it is getting old.

Look at this series of posts in this thread. Nyikos didn't even tell
me that he had delivered his third knockdown, and he still hasn't
What kind of person would do that after a year and a half of threats
and boasting about it? These aren't the only posts Nyikos has posted
to me since he delivered his third knockdown attempt. Reality is that
tragically stupid.

>
> If he really is aware of his own transgressions then it seems likely
> he's looking for attention, and in that case the best thing to do is
> deny him that. But if, as I believe, he cannot help himself, then
> squabbling with him is not only undesirable, it's unkind. In either
> case it seems to me you benefit by just letting things drop.

Who is the one that keeps posting to me? He did claim that he would
stop after delivering his third knockdown, but he lied. I have no
doubt that he can't help himself. I can only tell him to go away in a
language that I know that he understands. Countering his delusions is
the only thing that makes him stop for any period of time. The truth
is something that he can't deal with.

Ron Okimoto

[Roger Shrubber]

Ron O wrote:
> On Apr 12, 7:57 pm, Mark Isaak <eci...@curioustax.onomy.net> wrote:

>> ... whines about lots of people. In doing so, he tells all but the

>> most socially illiterate readers a lot about himself and little or
>> nothing about whom he is whining about.
>
> It has become my experience that this is not the case for all people
> who want to comment on the situation when they are obviously ignorant
> of the situation, or have reasons of their own for encouraging the
> boob.

You presume that objecting to you frequently using a flamethrower
to control aphids in the garden is our ignorance of the problem
of aphids.

Your response does not help the situation. In fact, it makes
it worse. So people ask you to stop.

[Ron O]

You knew better. End of story. You blundered in of your own free
will, and your own reasons.

Poor Nyikos, reduced to being an aphid in the garden. This is non
flamethrower language? I should practice up.

Ron Okimoto

[Roger Shrubber]

You're demonstrating your inability to respond rationally, extending
the perception that you've lost all perspective. You'll note I omitted
names but you insist on adding them. You'll note you insist on
extending the metaphor as an attack on somebody else rather than an
illustration of a counterproductive response. You have chosen to
leverage your post into an attack on somebody who is not directly
involved in the conversation. You've anointed yourself with the
oil of sanctimonious moral high ground and pretend it is a valid
defense for any and all of your actions.

Most of the rest of us do not partake of your religious conviction
to absolve you of any guilt for your own actions because you
are engaged in a holy jihad.

Your sin, in my eyes, and I expect in the eyes of others, is
zealotry. Look at your words above. You accuse people of not
understanding how your adversary behaves. This is not true.
They repeatedly tell you as much but you repeat the accusation.
We disagree that yours is an appropriate response. We tell you
it is a counter-productive response. You respond to us that
we don't understand that your adversary is evil. You tell
yourself we must not understand how evil your adversary is
or else we would not object to your behavior. You refuse to
consider that we know exactly what is going on and have seen
the invidious accusations that people are a danger to their
own children. I know. On a purely pragmatic level, it does
not excuse your behavior. Your responses fail, and not because
we are ignorant of how you and others have been attacked.

If you took out the flamethrower once a year or so, I
it would be different. But you're like a fool who drops
an F-bomb in every other sentence and doesn't understand
that it does not enhance but rather detracts from everything
they have to say.

[jillery]

There is very good evidence of other posters enabling rockhead's
behavior, so that argument is out. Also, rockhead's bad behavior
remains whether he gets attention or not, so that argument is out.
Also, "maintains a substantive discussion" applies only if one ignores
all of the obfuscating noise, the chronic references to past posts,
the incoherent scrambling of other posters' text, and the continuous
peppering of personal insults, so that argument is out.

What else you got?

[jillery]

On Sat, 13 Apr 2013 13:40:52 +0930, Roger Shrubber
<rog.sh...@gmail.com> wrote:

>Ron O wrote:
>> On Apr 12, 7:57 pm, Mark Isaak <eci...@curioustax.onomy.net> wrote:
>
>
>>> ... whines about lots of people. In doing so, he tells all but the
>>> most socially illiterate readers a lot about himself and little or
>>> nothing about whom he is whining about.
>>
>> It has become my experience that this is not the case for all people
>> who want to comment on the situation when they are obviously ignorant
>> of the situation, or have reasons of their own for encouraging the
>> boob.
>
>You presume that objecting to you frequently using a flamethrower
>to control aphids in the garden is our ignorance of the problem
>of aphids.

Your is an interesting analogy, that of a sap sucking parasite.
Regarding your characterization of what you think Ron presumes, he did
identify two separate cases. To that list I add willfull denial and
deliberate dismissal of the problem.

>Your response does not help the situation. In fact, it makes
>it worse. So people ask you to stop.

Even if that is a fair characterization, which I don't believe it is,
I don't see how it makes the problem worse. OTOH how does ignoring
aphids help? Aphids don't suck sap because they seek attention.
Perhaps you have a very different idea of what the problem actually
is, but you haven't articulated it.

[alias Ernest Major]

One example would be the monophyly of Archaeplastida (red algae,
glaucophytes, green algae and "land" plants). I have the impression that
the widespread acceptance of this as a clade has a lot to do with a
"morphological" trait (possession of primary plastids). However the
molecular data is so far far from clear cut on relationships among
non-excavate bikonts (Corticata).

Plastids appear to form a clade within cyanobacteria, from which it is
inferred that endosymbiosis occurred only once, and Archaeplastida are
monophyletic. Alternative hypotheses include

1) Endosymbiosis occurred several times involving a clade of
cyanobacteria no longer extant (or not yet sampled).

2) Endosymbiosis occurred several times involving several cyanobacterial
clades and plastid monophyly is only apparent. Convergence does occur in
plastid evolution - for example the same genes have been lost from the
plastome in several different plant clades. The question is whether it
is plausible that this could result in sufficient convergence at the
sequence level.

3) Some Archaeplastids (putatively some or all of Hacrobia) lost their
primary plastids, and subsquently gained secondary plastids.

--
alias Ernest Major