Avian Respiration and Evolution

[jillery]

Perhaps this newsgroup is a better place to discuss this after all.

I ran across these ScienceDaily articles:

<http://www.sciencedaily.com/releases/2010/02/100209183335.htm>

birds are not evolved from dinosaurs, but that some dinosaurs may be
evolved from birds, and:

<http://www.sciencedaily.com/releases/2009/06/090609092055.htm>

extant birds hold their femurs semi-horizontally, to support their
internal air sacs, while apparently theropod dinosaurs did not, making
it unlikely birds arose from theropod dinosaurs.

The above is based on the following research report:

<http://onlinelibrary.wiley.com/doi/10.1002/jmor.10752/pdf>


Contrasting with the above, I found this:

<http://www.sciencedaily.com/releases/2007/11/071107074326.htm>

breathing structures, known as uncinate processes, are also present in
maniraptoran dinosaurs and Archaeopteryx.

The above is based on the following research report:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596187/

I freely admit most of this is new to me, that when birds walk, they
hold their hips more or less in place while rotating their knees over
a large angle. In contrast, most mammals move their hips over a much
larger angle than do birds, even nonflying birds. Apparently even
penguins stand in a kind of squat, with their thighs close to the
abdomen and their knees bent.

According to Quick and Ruben, this adaptation is necessary in order to
support the posterior air sac during inspiration, that auxiliary
structures like gastralia and uncinate processes don't prevent its
paradoxical collapse. But theropod dinosaurs, from which birds are
supposed to have evolved, including velociraptors and Archaeopteryx,
didn't have this limitation, but stood with their knees more-or-less
straight, a very unavian posture.

So, assuming the above anatomical statements are correct, does that
necessarily mean birds did not evolve from dinosaurs? Or that some
dinosaurs evolved from birds? Isn't it plausible that this anatomical
requirement became necessary after birds evolved powered flight? Is
this a big question in the scientific community?

[Richard Norman]

On Fri, 21 Sep 2012 08:01:12 -0400, jillery <69jp...@gmail.com>
wrote:

Thank you for raising this controversy here and especially by
providing the original research papers rather than merely the press
releases. I might add one more. You cite the most recent of the two
Ruben papers mentioned in the two ScienceDaily posts. Just for the
sake of completeness, the other is
http://onlinelibrary.wiley.com/doi/10.1002/jmor.10752/pdf

As a physiology I am generally familiar with respiratory, circulatory,
and locomotory mechanisms of modern animals but not all the gory
anatomical or paleontological details which are all-essential here so
I have to do some reading and studying to answer more properly. John
Harshman is really the bird evolution specialist and should be able to
answer you properly.

But what I do find are powerful objections to the dissenting view of
Ruben and his co-workers. For example the Darren Naish blog
"Publishing with a hidden agenda: why birds simply cannot be
dinosaurs" at

http://scienceblogs.com/tetrapodzoology/2009/07/17/birds-cannot-be-dinosaurs/

Naish writes: "Ruben and colleagues seem to have made a career of
publishing papers in which they assert that ‘birds cannot be dinosaurs
because of [insert supposed fatal flaw in the 'birds are dinosaurs'
model]‘, and there’s no indication that criticism of their conclusions
will cause them to stop now. However, a brief discussion held over at
Penguinology has changed my mind: we should try and set the record
straight. Or, with great power comes great responsbility, or whatever.
What makes this research particularly grating is that, like all the
other papers by Ruben, Feduccia, Martin and colleagues, the ‘birds are
not dinosaurs’ movement relies on two under-handed tricks that should
be exposed."

More to the point, a recent paper on "Evolution of the Respiratory
System in Nonavian Theropods: Evidence from Rib and Vertebral
Morphology" concludes "these data lead us to conclude that an
avian-style pulmonary system was likely a universal theropod trait."
That is, Ruben is wrong.
http://onlinelibrary.wiley.com/doi/10.1002/ar.20989/pdf

That paper begins: "Several recent studies on the evolutionary history
of the avian respiratory system have indicated that several characters
that define modern avian respiration extend back into the nonavian
theropod lineage, possibly indicating the group had a more avian-like
respiratory system (O’Connor, 2004, 2006; O’Connor and Claessens,
2005). Given the strong support for the placement of theropod
dinosaurs between modern birds and crocodilians, the extant
phylogenetic bracket (EPB) method (Witmer, 1995a) could potentially be
used to provide further support for a more avian-like respiratory
system in nonavian theropods."

Also, Rubens objections seem to be based on crocodilian breathing
mechanisms but another paper argues that crocodilians are exceptions
and that a form of pulmonary air sacs may have been primitive.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0034094

It seems that the papers you found about "birds are not dinosaurs" is
a very minority view, the last gasp of a dying breed. Of course the
creationist/intelligent design community has seized on this argument
as proof that evolution must be wrong.

[jillery]

Actually, this is the same one I posted. If there is another Ruben
paper, I would like to read that as well.

Is this the other article had in mind? Darren Naish mentioned it in
the blog you cited:

<http://www.sonoma.edu/users/g/geist/Scipionyx.pdf>

Thank your for these links and your comments. I couldn't tell from
the articles where Ruben was coming from, whether he used to think
bird are dinosaurs but changed his mind, or whether he never thought
birds are dinosaurs.

As for ID/Creationists, sometimes they are so anxious to prove Science
Is Wrong (c), that they seem not to realize they are arguing against
their own fundamental assumptions.

Is it your understanding that Ruben is one of them?

[Richard Norman]

On Fri, 21 Sep 2012 10:46:12 -0400, jillery <69jp...@gmail.com>

Sorry about the reference. I had too many windows open at one time
and picked the wrong one. The other article (not a real research
paper) from PNAS mentioned in ScienceDaily is
http://www.pnas.org/content/107/7/2733.full

Ruben is most definitely not an anti-evolutionist. He is merely of
the "old school" when birds were not dinosaurs at all.

When creationists yell at school boards to "teach the controvery",
they somehow never mean to teach about real controversies within
science which do exist but rather made-up controversies between
science and anti-science.

[John Harshman]

On 9/21/12 2:01 PM, jillery wrote:
> Perhaps this newsgroup is a better place to discuss this after all.
>
> I ran across these ScienceDaily articles:
>
> <http://www.sciencedaily.com/releases/2010/02/100209183335.htm>
>
> birds are not evolved from dinosaurs, but that some dinosaurs may be
> evolved from birds, and:
>
> <http://www.sciencedaily.com/releases/2009/06/090609092055.htm>
>
> extant birds hold their femurs semi-horizontally, to support their
> internal air sacs, while apparently theropod dinosaurs did not, making
> it unlikely birds arose from theropod dinosaurs.
>
> The above is based on the following research report:
>
> <http://onlinelibrary.wiley.com/doi/10.1002/jmor.10752/pdf>
>
>
> Contrasting with the above, I found this:
>
> <http://www.sciencedaily.com/releases/2007/11/071107074326.htm>
>
> breathing structures, known as uncinate processes, are also present in
> maniraptoran dinosaurs and Archaeopteryx.
>
> The above is based on the following research report:
>
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596187/
>
> I freely admit most of this is new to me, that when birds walk, they
> hold their hips more or less in place while rotating their knees over
> a large angle.

What you mean is that the femur rotates through a small angle and the
tibiotarsus through a large angle. And that's correct, for all birds.

> In contrast, most mammals move their hips over a much
> larger angle than do birds, even nonflying birds.

Nonflying birds are no different in this respect from flying birds. And
of course mammals move their femurs over a large angle.

> Apparently even
> penguins stand in a kind of squat, with their thighs close to the
> abdomen and their knees bent.
>
> According to Quick and Ruben, this adaptation is necessary in order to
> support the posterior air sac during inspiration, that auxiliary
> structures like gastralia and uncinate processes don't prevent its
> paradoxical collapse. But theropod dinosaurs, from which birds are
> supposed to have evolved, including velociraptors and Archaeopteryx,
> didn't have this limitation, but stood with their knees more-or-less
> straight, a very unavian posture.

Which apparently demonstrates conclusively that Archaeopteryx is not a
bird. That's one problem with BANDits: they can't agree on where the
line between birds (not dinosaurs) and dinosaurs (not birds) is; it
varies from publication to publication, with the only common conclusion
that birds are not dinosaurs, are not are not are not.

> So, assuming the above anatomical statements are correct, does that
> necessarily mean birds did not evolve from dinosaurs? Or that some
> dinosaurs evolved from birds? Isn't it plausible that this anatomical
> requirement became necessary after birds evolved powered flight? Is
> this a big question in the scientific community?

To answer the last question first: no. Ruben has spent his career
finding this or that anatomical detail that supposedly prevents birds
from possibly being dinosaurs. Since it's obvious from phylogenetic
analyses that birds are in fact dinosaurs, nobody in the field pays much
attention. It's all special pleading. Somewhere, though I can't
immediately find the source, there's a response that shows the whole
"paradoxical collapse" idea to be flawed. Maybe your googling is better
than mine.

As a good rule of thumb, you may suppose that anything with John Ruben's
name on it is wrong.

[jillery]

I'm glad you're willing and able to translate my inexpertese for me.

>> In contrast, most mammals move their hips over a much
>> larger angle than do birds, even nonflying birds.
>
>Nonflying birds are no different in this respect from flying birds. And
>of course mammals move their femurs over a large angle.

Of course. My emphasis here is this appears to be an obligate
condition unaltered by lifestyle. When I first heard about this, I
imagined ratites would run faster if they moved their femur over a
larger angle. Now I know why they can't do that.

>> Apparently even
>> penguins stand in a kind of squat, with their thighs close to the
>> abdomen and their knees bent.
>>
>> According to Quick and Ruben, this adaptation is necessary in order to
>> support the posterior air sac during inspiration, that auxiliary
>> structures like gastralia and uncinate processes don't prevent its
>> paradoxical collapse. But theropod dinosaurs, from which birds are
>> supposed to have evolved, including velociraptors and Archaeopteryx,
>> didn't have this limitation, but stood with their knees more-or-less
>> straight, a very unavian posture.
>
>Which apparently demonstrates conclusively that Archaeopteryx is not a
>bird. That's one problem with BANDits: they can't agree on where the
>line between birds (not dinosaurs) and dinosaurs (not birds) is; it
>varies from publication to publication, with the only common conclusion
>that birds are not dinosaurs, are not are not are not.

And humans are not apes.

>> So, assuming the above anatomical statements are correct, does that
>> necessarily mean birds did not evolve from dinosaurs? Or that some
>> dinosaurs evolved from birds? Isn't it plausible that this anatomical
>> requirement became necessary after birds evolved powered flight? Is
>> this a big question in the scientific community?
>
>To answer the last question first: no. Ruben has spent his career
>finding this or that anatomical detail that supposedly prevents birds
>from possibly being dinosaurs. Since it's obvious from phylogenetic
>analyses that birds are in fact dinosaurs, nobody in the field pays much
>attention. It's all special pleading. Somewhere, though I can't
>immediately find the source, there's a response that shows the whole
>"paradoxical collapse" idea to be flawed. Maybe your googling is better
>than mine.
>
>As a good rule of thumb, you may suppose that anything with John Ruben's
>name on it is wrong.

Sounds like good advice. Thank you for this information.

[pnyikos]

On Sep 21, 11:36 am, John Harshman <jharsh...@pacbell.net> wrote:
> On 9/21/12 2:01 PM, jillery wrote:

> > Perhaps this newsgroup is a better place to discuss this after all.

I'm glad jillery feels this way, and hope [s]he will be a regular
contributor of such items.

> > I ran across these ScienceDaily articles:
>
> > <http://www.sciencedaily.com/releases/2010/02/100209183335.htm>
>
> > birds are not evolved from dinosaurs, but that some dinosaurs may be
> > evolved from birds, and:

Actually the emphasis in the linked PNAS article is elsewhere (except
at the very end): that birds are evolved from arboreal gliders rather
than ground-dwelling runners ("cursorial"). The concluding paragraph
in the PNAS article, linked from the bottom of the above article, has
its first sentence following smoothly from what came before:

"So, is the answer, after all, a hybrid of the two old theories,
i.e., avian origins from an arboreal, gliding theropod dinosaur?"

But then, Ruben gets on the hobbyhorse that becomes an over-riding
feature of the Science Daily article.

"Perhaps, but then this is paleobiology—very recent data suggest that
many clearly cursorial theropods previously thought to have been
feathered may not have been so (14) and that dromaeosaurs, the group
that birds are assumed to have been derived from, may not even have
been dinosaurs (15). What pops up next is anyone’s guess."

The bit after "Perhaps" seems disconnected from the rest of the
article, but the part after "(14)" is also what the Science Daily
aricle lays the greatest emphasis on.

> > <http://www.sciencedaily.com/releases/2009/06/090609092055.htm>
>
> > extant birds hold their femurs semi-horizontally, to support their
> > internal air sacs, while apparently theropod dinosaurs did not, making
> > it unlikely birds arose from theropod dinosaurs.
>
> > The above is based on the following research report:
>
> > <http://onlinelibrary.wiley.com/doi/10.1002/jmor.10752/pdf>
>
> > Contrasting with the above, I found this:
>
> > <http://www.sciencedaily.com/releases/2007/11/071107074326.htm>
>
> > breathing structures, known as uncinate processes, are also present in
> > maniraptoran dinosaurs and Archaeopteryx.
>
> > The above is based on the following research report:
>
> >http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596187/
>
> > I freely admit most of this is new to me, that when birds walk, they
> > hold their hips more or less in place while rotating their knees over
> > a large angle.
>
> What you mean is that the femur rotates through a small angle and the
> tibiotarsus through a large angle. And that's correct, for all birds.

Is the tibiotarsus homologous to our knees? What's the word "tarsus"
doing in there?

> > In contrast, most mammals move their hips over a much
> > larger angle than do birds, even nonflying birds.
>
> Nonflying birds are no different in this respect from flying birds. And
> of course mammals move their femurs over a large angle.

What about true ("earless") seals?

> > Apparently even
> > penguins stand in a kind of squat, with their thighs close to the
> > abdomen and their knees bent.
>
> > According to Quick and Ruben, this adaptation is necessary in order to
> > support the posterior air sac during inspiration, that auxiliary
> > structures like gastralia and uncinate processes don't prevent its
> > paradoxical collapse.  But theropod dinosaurs, from which birds are
> > supposed to have evolved, including velociraptors and Archaeopteryx,
> > didn't have this limitation, but stood with their knees more-or-less
> > straight, a very unavian posture.
>
> Which apparently demonstrates conclusively that Archaeopteryx is not a
> bird.

I take it you are being ironic here. Archaeopteryx has never been
ruled out as a common ancestor of all extant birds, has it?

That's not to say that it will ever be shown to *be* a common ancestor
(at least not to the satisfaction of cladists, to whom lack of access
to a complete specimen is enough to rule out such a "showing"). Nor
is it to say that it is a candidate for the *last* common ancestor--it
clearly is not.

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 9/28/12 8:01 PM, pnyikos wrote:
> On Sep 21, 11:36 am, John Harshman<jharsh...@pacbell.net> wrote:

>> What you mean is that the femur rotates through a small angle and the
>> tibiotarsus through a large angle. And that's correct, for all birds.
>
> Is the tibiotarsus homologous to our knees?

No. The knee is a joint, not a bone. The knee is the joint between the
femur and the tibia/fibula.

> What's the word "tarsus"
> doing in there?

And "tarsus" means "ankle". Birds have more or less the same ankle bones
we do, but they work differently. And they have a lot of fusion of
bones. Some of the bird's ankle bones are fused to the tibia; ergo,
"tibiotarsus". The rest of the ankle bones are fused to the metatarsals,
bones of the foot; ergo, "tarsometatarsus".

>>> In contrast, most mammals move their hips over a much
>>> larger angle than do birds, even nonflying birds.
>>
>> Nonflying birds are no different in this respect from flying birds. And
>> of course mammals move their femurs over a large angle.
>
> What about true ("earless") seals?

Yeah, and what about whales? Most of them don't even have femurs, so there.

>>> Apparently even
>>> penguins stand in a kind of squat, with their thighs close to the
>>> abdomen and their knees bent.
>>
>>> According to Quick and Ruben, this adaptation is necessary in order to
>>> support the posterior air sac during inspiration, that auxiliary
>>> structures like gastralia and uncinate processes don't prevent its
>>> paradoxical collapse. But theropod dinosaurs, from which birds are
>>> supposed to have evolved, including velociraptors and Archaeopteryx,
>>> didn't have this limitation, but stood with their knees more-or-less
>>> straight, a very unavian posture.
>>
>> Which apparently demonstrates conclusively that Archaeopteryx is not a
>> bird.
>
> I take it you are being ironic here.

Good catch.

> Archaeopteryx has never been
> ruled out as a common ancestor of all extant birds, has it?

Do you really want to start that argument again? Trying to assign
ancestry to taxa is a useless exercise.

> That's not to say that it will ever be shown to *be* a common ancestor
> (at least not to the satisfaction of cladists, to whom lack of access
> to a complete specimen is enough to rule out such a "showing").

I have no idea where you could ever have got that notion. It isn't lack
of a complete specimen that's the problem. Now in fact Archaeopteryx has
autapomorphies that argue against it being the ancestor.

> Nor
> is it to say that it is a candidate for the *last* common ancestor--it
> clearly is not.

Well, I'm glad that's settled.

[jillery]

On Fri, 28 Sep 2012 20:01:03 -0700 (PDT), pnyikos
<nyi...@bellsouth.net> wrote:

>On Sep 21, 11:36 am, John Harshman <jharsh...@pacbell.net> wrote:
>> On 9/21/12 2:01 PM, jillery wrote:
>
>> > Perhaps this newsgroup is a better place to discuss this after all.
>
>I'm glad jillery feels this way, and hope [s]he will be a regular
>contributor of such items.

It's like you just can't help yourself. Thank you for reminding me
that Agent needs me to apply asshole filters on each newsgroup.

[John Harshman]

I'm a bit confused. What exactly did Peter do here (and I mean just in
that post) that merits an asshole filter?

[jillery]

If you're really interested, email me.

[Richard Norman]

On Sun, 30 Sep 2012 18:45:11 -0400, jillery <69jp...@gmail.com>
wrote:

(I've been away for a few days so I just saw this...)
This is simply Peter's somewhat formal way of being nice. I don't see
any negative intonation whatsoever.

[jillery]

Your opinion is noted. Why you think it matters?

[Richard Norman]

On Tue, 02 Oct 2012 01:23:42 -0400, jillery <69jp...@gmail.com>

wrote:

>On Mon, 01 Oct 2012 18:07:07 -0400, Richard Norman
><r_s_n...@comcast.net> wrote:
>
>>On Sun, 30 Sep 2012 18:45:11 -0400, jillery <69jp...@gmail.com>
>>wrote:
>>
>>>On Fri, 28 Sep 2012 20:01:03 -0700 (PDT), pnyikos
>>><nyi...@bellsouth.net> wrote:
>>>
>>>>On Sep 21, 11:36�am, John Harshman <jharsh...@pacbell.net> wrote:
>>>>> On 9/21/12 2:01 PM, jillery wrote:
>>>>
>>>>> > Perhaps this newsgroup is a better place to discuss this after all.
>>>>
>>>>I'm glad jillery feels this way, and hope [s]he will be a regular
>>>>contributor of such items.
>>>
>>>
>>>It's like you just can't help yourself. Thank you for reminding me
>>>that Agent needs me to apply asshole filters on each newsgroup.
>>
>>(I've been away for a few days so I just saw this...)
>>This is simply Peter's somewhat formal way of being nice. I don't see
>>any negative intonation whatsoever.
>
>
>Your opinion is noted. Why you think it matters?

It doesn't. It is just that i am as dense as John Harshman about
this.

[pnyikos]

On Oct 2, 7:39 am, Richard Norman <r_s_nor...@comcast.net> wrote:
> On Tue, 02 Oct 2012 01:23:42 -0400, jillery <69jpi...@gmail.com>

> wrote:
>
>
>
>
>
>
>
>
>
> >On Mon, 01 Oct 2012 18:07:07 -0400, Richard Norman

> ><r_s_nor...@comcast.net> wrote:
>
> >>On Sun, 30 Sep 2012 18:45:11 -0400, jillery <69jpi...@gmail.com>

> >>wrote:
>
> >>>On Fri, 28 Sep 2012 20:01:03 -0700 (PDT), pnyikos
> >>><nyik...@bellsouth.net> wrote:
>
> >>>>On Sep 21, 11:36 am, John Harshman <jharsh...@pacbell.net> wrote:
> >>>>> On 9/21/12 2:01 PM, jillery wrote:
>
> >>>>> > Perhaps this newsgroup is a better place to discuss this after all.
>
> >>>>I'm glad jillery feels this way, and hope [s]he will be a regular
> >>>>contributor of such items.
>
> >>>It's like you just can't help yourself.  Thank you for reminding me
> >>>that Agent needs me to apply asshole filters on each newsgroup.
>
> >>(I've been away for a few days so I just saw this...)
> >>This is simply Peter's somewhat formal way of being nice.  I don't see
> >>any negative intonation whatsoever.
>
> >Your opinion is noted.  Why you think it matters?
>
> It doesn't.  It is just that i am as dense as John Harshman about
> this.

I was being completely sincere, Richard. The way I see it, getting
sci.bio.paleontology back to its original subject matter should take
precedence over personal clashes.

I sometimes get personal even here, as you saw where John Harshman and
"people are fish" is concerned, but that comes only after a thread is
established here with on-topic material to which I, too, have
contributed.

Well, almost always. I made an exception for that "people are fish"
brouhaha, but only because that harked back to an earlier
sci.bio.paleontology thread.

By the way, you are still a bit in the dark about one thing: It was I,
NOT John, who introduced the "people are fish" bit. It was intended
as a satire on the "people are apes" bit, which so many non-
creationists seem to be quite serious about.

Perhaps you are correct in thinking that the intent *always* is to
tweak creationists [and hence it comes under jillery's broad
definition of trolling] in which case my satire was misdirected, but I
did get the impression that some people were quite insistent about
humans being apes, and I decided to satirize that by posting what I
did about "The Incredible Mr. Limpet."

By the way, jillery killfiled me in talk.origins long ago, and it
looks like [s]he has killfiled me here too. As to why, I'm sure 'e
has a completely different explanation than I do. Just be aware that
you will be hearing only one side of the story from jilllery.

[pnyikos]

On Sep 30, 7:59 pm, John Harshman <jharsh...@pacbell.net> wrote:
> On 9/30/12 3:45 PM, jillery wrote:
>
> > On Fri, 28 Sep 2012 20:01:03 -0700 (PDT), pnyikos

> > <nyik...@bellsouth.net>  wrote:

>
> >> On Sep 21, 11:36 am, John Harshman<jharsh...@pacbell.net>  wrote:
> >>> On 9/21/12 2:01 PM, jillery wrote:
>
> >>>> Perhaps this newsgroup is a better place to discuss this after all.
>
> >> I'm glad jillery feels this way, and hope [s]he will be a regular
> >> contributor of such items.
>
> > It's like you just can't help yourself.  Thank you for reminding me
> > that Agent needs me to apply asshole filters on each newsgroup.
>
> I'm a bit confused. What exactly did Peter do here (and I mean just in
> that post) that merits an asshole filter?

Absolutely nothing. See my reply to Richard Norman of a few minutes
ago.

"jillery" asked you to e-mail her/him about it, but I advise against
it, for reasons mentioned in the last paragraph of my reply to
Richard.

Incidentally, my use of "[s]he" harks back to one of my very first
posts after my decade-long break, when I asked jillery, "Are you a
woman?" and added something to the effect of "If you are, let me
compliment you for posting to what is an overwhelmingly male-dominated
newsgroup."

Apparently jillery took that the wrong way for no discernible reason,
and has never answered the question even when others have asked. Not
wishing to guess wrong, I've used gender-neutral language ever since.

Peter Nyikos

[jillery]

On Tue, 02 Oct 2012 07:39:17 -0400, Richard Norman

<r_s_n...@comcast.net> wrote:

>On Tue, 02 Oct 2012 01:23:42 -0400, jillery <69jp...@gmail.com>
>wrote:
>
>>On Mon, 01 Oct 2012 18:07:07 -0400, Richard Norman
>><r_s_n...@comcast.net> wrote:
>>
>>>On Sun, 30 Sep 2012 18:45:11 -0400, jillery <69jp...@gmail.com>
>>>wrote:
>>>
>>>>On Fri, 28 Sep 2012 20:01:03 -0700 (PDT), pnyikos
>>>><nyi...@bellsouth.net> wrote:
>>>>
>>>>>On Sep 21, 11:36�am, John Harshman <jharsh...@pacbell.net> wrote:
>>>>>> On 9/21/12 2:01 PM, jillery wrote:
>>>>>
>>>>>> > Perhaps this newsgroup is a better place to discuss this after all.
>>>>>
>>>>>I'm glad jillery feels this way, and hope [s]he will be a regular
>>>>>contributor of such items.
>>>>
>>>>
>>>>It's like you just can't help yourself. Thank you for reminding me
>>>>that Agent needs me to apply asshole filters on each newsgroup.
>>>
>>>(I've been away for a few days so I just saw this...)
>>>This is simply Peter's somewhat formal way of being nice. I don't see
>>>any negative intonation whatsoever.
>>
>>

>>Your opinion is noted. Why [do] you think it matters?
>
>It doesn't.


Then you and I agree.

>It is just that i am as dense as John Harshman about
>this.

You just agreed your opinion doesn't matter, and yet you continue to
press the point. Do you think this is the right time and place to
pursue irrelevant, off-topic, non-scientific issues? Do you think
this is the right way to pursue *this* point?

To be clear, on both questions, I don't.

[Richard Norman]

On Tue, 02 Oct 2012 16:16:40 -0400, jillery <69jp...@gmail.com>

Apparently I thought it so because I did it. The reason why I did it
is another story altogether. You don't think it important yet you
still continue to press the point. Is that different somehow?

[jillery]

On Tue, 02 Oct 2012 16:18:09 -0400, Richard Norman

I maintain my right to reply to your posts as I choose. Since you
want to continue with this irrelevant, off-topic, and non-scientific
thread, I can accomodate you.

[pnyikos]

On Sep 29, 12:50 am, John Harshman <jharsh...@pacbell.net> wrote:
> On 9/28/12 8:01 PM, pnyikos wrote:
>
> > On Sep 21, 11:36 am, John Harshman<jharsh...@pacbell.net>  wrote:

> > > jillery wrote:

> > >> <http://www.sciencedaily.com/releases/2009/06/090609092055.htm>

> > >> I freely admit most of this is new to me, that when birds walk,
> > >> they hold their hips more or less in place while rotating

> > >> their knees over a large angle.

> >> What you mean is that the femur rotates through a small angle and the
> >> tibiotarsus through a large angle. And that's correct, for all birds.

It seems pretty clear from the linked article that this is NOT what
the linked article meant, and so jillery probably did not mean it
either. The picture accompanying the linked article labeled both the
hip and the knee joints, using colors to highlight them.

By the way, when you said "rotates" did you mean around the long
axis? I don't think you did, but that illustrates how the article
and jillery were unambiguous, while you were not.

> > Is the tibiotarsus homologous to our knees?
>
> No. The knee is a joint, not a bone. The knee is the joint between the
> femur and the tibia/fibula.

> > What's the word "tarsus"
> > doing in there?
>
> And "tarsus" means "ankle". Birds have more or less the same ankle bones
> we do, but they work differently. And they have a lot of fusion of
> bones.

Yeah, I was really surprised to see that birds fuse THREE metatarsals;
I'd only heard about cannon bones of camelids and some deer (not
horses, where there is only one metatarsal besides the narrow splints)
before, and those only fuse two.

Spurred by this article, I did some browsing in Romer's _Vertebrate
Paleontology_ and saw that ornithomimids also fused three metatarsals,
strengthening the case for birds being (descended from) dinosaurs.

> Some of the bird's ankle bones are fused to the tibia; ergo,
> "tibiotarsus". The rest of the ankle bones are fused to the metatarsals,
> bones of the foot; ergo, "tarsometatarsus".
>
> >>> In contrast, most mammals move their hips over a much
> >>> larger angle than do birds, even nonflying birds.
>
> >> Nonflying birds are no different in this respect from flying birds. And
> >> of course mammals move their femurs over a large angle.
>
> > What about true ("earless") seals?
>
> Yeah, and what about whales? Most of them don't even have femurs, so there.

Have you decided to go all childish and smart-alecky when people point
out possible exceptions to what you write?

Here's another possible REAL exception: when bats crawl along on
horizontal surfaces, their hind legs are so twisted, it really looks
like their knees bend the wrong way. [Reminds me of another recent
s.b.p. thread.]

> >>> Apparently even
> >>> penguins stand in a kind of squat, with their thighs close to the
> >>> abdomen and their knees bent.
>
> >>> According to Quick and Ruben, this adaptation is necessary in order to
> >>> support the posterior air sac during inspiration, that auxiliary
> >>> structures like gastralia and uncinate processes don't prevent its
> >>> paradoxical collapse.  But theropod dinosaurs, from which birds are
> >>> supposed to have evolved, including velociraptors and Archaeopteryx,
> >>> didn't have this limitation, but stood with their knees more-or-less
> >>> straight, a very unavian posture.
>
> >> Which apparently demonstrates conclusively that Archaeopteryx is not a
> >> bird.
>
> > I take it you are being ironic here.
>
> Good catch.
>
> > Archaeopteryx has never been
> > ruled out as a common ancestor of all extant birds, has it?
>
> Do you really want to start that argument again? Trying to assign
> ancestry to taxa is a useless exercise.

False dichotomy. There's a huge gray area between "prove" and "rule
out".

> > That's not to say that it will ever be shown to *be* a common ancestor
> > (at least not to the satisfaction of cladists, to whom lack of access
> > to a complete specimen is enough to rule out such a "showing").
>
> I have no idea where you could ever have got that notion.

From you. You keep harping on the fact that even what looks like
direct ancestry from fossils could easily be falsified with more
complete data.

> It isn't lack
> of a complete specimen that's the problem. Now in fact Archaeopteryx has
> autapomorphies that argue against it being the ancestor.

Ah, but are those autapomorphies significant enough to argue against
some other species of Archaeopteryx than the ones discovered so far
being direct ancestors?

I realize I am treading on controversial ground here: once upon a
time, the Berlin specimen of Archaeopteryx was given a whole new
genus, Archaeornis. The splitters lost out on that one, big-time:
they are even considered to be the same species these days.

> > Nor
> > is it to say that it is a candidate for the *last* common ancestor--it
> > clearly is not.
>
> Well, I'm glad that's settled.

Are you ironically implying that it still hasn't been ruled out as the
LCA?

Bad catch this time, I fear.

[John Harshman]

On 10/5/12 10:38 AM, pnyikos wrote:
> On Sep 29, 12:50 am, John Harshman<jharsh...@pacbell.net> wrote:
>> On 9/28/12 8:01 PM, pnyikos wrote:
>>
>>> On Sep 21, 11:36 am, John Harshman<jharsh...@pacbell.net> wrote:
>>>> jillery wrote:
>
>>>>> <http://www.sciencedaily.com/releases/2009/06/090609092055.htm>
>
>>>>> I freely admit most of this is new to me, that when birds walk,
>>>>> they hold their hips more or less in place while rotating
>>>>> their knees over a large angle.
>
>>>> What you mean is that the femur rotates through a small angle and the
>>>> tibiotarsus through a large angle. And that's correct, for all birds.
>
> It seems pretty clear from the linked article that this is NOT what
> the linked article meant, and so jillery probably did not mean it
> either. The picture accompanying the linked article labeled both the
> hip and the knee joints, using colors to highlight them.

I fail to see how a hip joint can move. And the knee joint moves exactly
to the extent that the femur does. Anyway, you misunderstand the intent
of the diagram, which appears to be merely to locate the joints. It
should be clear from the text that "movement around the hip joint" means
"movement of the femur", "movement around the knee joint means "movement
of the tibiotarsus", and "movement around the ankle joint" means
"movement of the tarsometatarsus". "Movement of the joint" is quite
different from "movement around the joint". A bird's knee moves very
little, because the femur moves very little. A bird's ankle moves quite
a lot, because the tibiotarsus moves quite a lot. Is that clear now?

> By the way, when you said "rotates" did you mean around the long
> axis? I don't think you did, but that illustrates how the article
> and jillery were unambiguous, while you were not.

As is so often the case, you have difficulty interpreting simple
statements. The usual technical term is "excursion". But yes, I meant
around the long axis.

>>> Is the tibiotarsus homologous to our knees?
>>
>> No. The knee is a joint, not a bone. The knee is the joint between the
>> femur and the tibia/fibula.
>
>>> What's the word "tarsus"
>>> doing in there?
>>
>> And "tarsus" means "ankle". Birds have more or less the same ankle bones
>> we do, but they work differently. And they have a lot of fusion of
>> bones.
>
> Yeah, I was really surprised to see that birds fuse THREE metatarsals;
> I'd only heard about cannon bones of camelids and some deer (not
> horses, where there is only one metatarsal besides the narrow splints)
> before, and those only fuse two.
>
> Spurred by this article, I did some browsing in Romer's _Vertebrate
> Paleontology_ and saw that ornithomimids also fused three metatarsals,
> strengthening the case for birds being (descended from) dinosaurs.

Not really, since the fusion was entirely convergent.

>> Some of the bird's ankle bones are fused to the tibia; ergo,
>> "tibiotarsus". The rest of the ankle bones are fused to the metatarsals,
>> bones of the foot; ergo, "tarsometatarsus".
>>
>>>>> In contrast, most mammals move their hips over a much
>>>>> larger angle than do birds, even nonflying birds.
>>
>>>> Nonflying birds are no different in this respect from flying birds. And
>>>> of course mammals move their femurs over a large angle.
>>
>>> What about true ("earless") seals?
>>
>> Yeah, and what about whales? Most of them don't even have femurs, so there.
>
> Have you decided to go all childish and smart-alecky when people point
> out possible exceptions to what you write?

No. I've decided to go all childish and smart-alecky when people raise
pointless exceptions that contribute nothing to the discussion.

> Here's another possible REAL exception: when bats crawl along on
> horizontal surfaces, their hind legs are so twisted, it really looks
> like their knees bend the wrong way. [Reminds me of another recent
> s.b.p. thread.]
>
>>>>> Apparently even
>>>>> penguins stand in a kind of squat, with their thighs close to the
>>>>> abdomen and their knees bent.
>>
>>>>> According to Quick and Ruben, this adaptation is necessary in order to
>>>>> support the posterior air sac during inspiration, that auxiliary
>>>>> structures like gastralia and uncinate processes don't prevent its
>>>>> paradoxical collapse. But theropod dinosaurs, from which birds are
>>>>> supposed to have evolved, including velociraptors and Archaeopteryx,
>>>>> didn't have this limitation, but stood with their knees more-or-less
>>>>> straight, a very unavian posture.
>>
>>>> Which apparently demonstrates conclusively that Archaeopteryx is not a
>>>> bird.
>>
>>> I take it you are being ironic here.
>>
>> Good catch.
>>
>>> Archaeopteryx has never been
>>> ruled out as a common ancestor of all extant birds, has it?
>>
>> Do you really want to start that argument again? Trying to assign
>> ancestry to taxa is a useless exercise.
>
> False dichotomy. There's a huge gray area between "prove" and "rule
> out".

Agreed. But there's a similar problem with certainty. Still, the cases
are not symmetrical: we can place a low probability on ancestry, but we
can almost never place a high probability. However, I don't see the
point of failing to rule out ancestry, since we learn nothing.

>>> That's not to say that it will ever be shown to *be* a common ancestor
>>> (at least not to the satisfaction of cladists, to whom lack of access
>>> to a complete specimen is enough to rule out such a "showing").
>>
>> I have no idea where you could ever have got that notion.
>
> From you. You keep harping on the fact that even what looks like
> direct ancestry from fossils could easily be falsified with more
> complete data.

You misunderstand. Nothing "looks like direct ancestry". There is no
such "showing".

>> It isn't lack
>> of a complete specimen that's the problem. Now in fact Archaeopteryx has
>> autapomorphies that argue against it being the ancestor.
>
> Ah, but are those autapomorphies significant enough to argue against
> some other species of Archaeopteryx than the ones discovered so far
> being direct ancestors?

Since any taxon "Archaeopteryx" would be arbitrarily delimited from
other birds, it's a meaningless question.

> I realize I am treading on controversial ground here: once upon a
> time, the Berlin specimen of Archaeopteryx was given a whole new
> genus, Archaeornis. The splitters lost out on that one, big-time:
> they are even considered to be the same species these days.

Actually, there's some question on that. But your apprehension is
meaningless.

>>> Nor
>>> is it to say that it is a candidate for the *last* common ancestor--it
>>> clearly is not.
>>
>> Well, I'm glad that's settled.
>
> Are you ironically implying that it still hasn't been ruled out as the
> LCA?

No. I'm expressing annoyance regarding your tendency to ruminate to
yourself in public. This is ruminating to yourself because the question
is of concern and relevance only to you.

> Bad catch this time, I fear.

Did you catch the ironic intent of "good catch"?

[jillery]

I think I'll walk away in bemusement.

[John Harshman]

I apologize to any other irony-impaired readers for their difficulty in
interpreting my remarks. But I refuse to employ emoticons. :)

[John Harshman]

On 10/6/12 4:17 AM, jillery wrote:

[jillery]

On Sat, 06 Oct 2012 08:25:17 -0700, John Harshman

You're right, Pnyikos doesn't deserve an apology over this.

[pnyikos]

On Oct 5, 7:38 pm, John Harshman <jharsh...@pacbell.net> wrote:
> On 10/5/12 10:38 AM, pnyikos wrote:
>
> > On Sep 29, 12:50 am, John Harshman<jharsh...@pacbell.net>  wrote:
> >> On 9/28/12 8:01 PM, pnyikos wrote:
>
> >>> On Sep 21, 11:36 am, John Harshman<jharsh...@pacbell.net>    wrote:
> >>>> jillery wrote:
>
> >>>>> <http://www.sciencedaily.com/releases/2009/06/090609092055.htm>
>
> >>>>> I freely admit most of this is new to me, that when birds walk,
> >>>>> they hold their hips more or less in place while rotating
> >>>>>   their knees over a large angle.
>
> >>>> What you mean is that the femur rotates through a small angle and the
> >>>> tibiotarsus through a large angle. And that's correct, for all birds.
>
> > It seems pretty clear from the linked article that this is NOT what
> > the linked article meant, and so jillery probably did not mean it
> > either.  The picture accompanying the linked article labeled both the
> > hip and the knee joints, using colors to highlight them.
>
> I fail to see how a hip joint can move. And the knee joint moves exactly
> to the extent that the femur does.

Yeah, but jillery didn't use the word "moving" but rather "rotating"
in connection with the knee joint.

> Anyway, you misunderstand the intent
> of the diagram, which appears to be merely to locate the joints. It
> should be clear from the text that "movement around the hip joint" means
> "movement of the femur",

Yes.

> "movement around the knee joint means "movement
> of the tibiotarsus",

Not if the femur is also moving. Then the tibiotarsus has two things
contributing to its movement, the other being the rotation of the knee
joint.

Oops, you'll claim this is a pointless exception that does nothing to
advance the discussion [as below], won't you?

> and "movement around the ankle joint" means
> "movement of the tarsometatarsus".

No comment.

> "Movement of the joint" is quite
> different from "movement around the joint".

Oh, wait! suddenly YOU are talking about the pointless exception of
the knee moving because the femur is moving, and not about the
movement around the knee.

> A bird's knee moves very
> little, because the femur moves very little. A bird's ankle moves quite
> a lot, because the tibiotarsus moves quite a lot. Is that clear now?

The only unclear thing is whether you'll go childish and smart-alecky
on account of my writing, "Not if the femur is also moving...."

> > By the way, when you said "rotates" did you mean around the long
> > axis?    I don't think you did, but that illustrates how the article
> > and jillery were unambiguous, while you were not.
>
> As is so often the case, you have difficulty interpreting simple
> statements. The usual technical term is "excursion". But yes, I meant
> around the long axis.

I'd call that twisting, not rotating. The long axis runs along the
length of the bone, the way we mathematicians use the words "long
axis".

[snip]

> > Yeah, I was really surprised to see that birds fuse THREE metatarsals;
> > I'd only heard about cannon bones of camelids and some deer (not
> > horses, where there is only one metatarsal besides the narrow splints)
> > before, and those only fuse two.
>
> > Spurred by this article, I did some browsing in  Romer's _Vertebrate
> > Paleontology_ and saw that ornithomimids also fused three metatarsals,
> > strengthening the case for birds being (descended from) dinosaurs.
>
> Not really, since the fusion was entirely convergent.

Did the other maniraptorans have it?

[snip]

> >>>>> In contrast, most mammals move their hips over a much
> >>>>> larger angle than do birds, even nonflying birds.
>
> >>>> Nonflying birds are no different in this respect from flying birds. And
> >>>> of course mammals move their femurs over a large angle.
>
> >>> What about true ("earless") seals?
>
> >> Yeah, and what about whales? Most of them don't even have femurs, so there.
>
> > Have you decided to go all childish and smart-alecky when people point
> > out possible exceptions to what you write?
>
> No. I've decided to go all childish and smart-alecky when people raise
> pointless exceptions that contribute nothing to the discussion.

Trouble is, I still don't know whether the lack of mobility of the
hind legs of seals is mainly to be blamed on the femur or the tibia/
fibula. Similarly for bats:

> > Here's another possible REAL exception: when bats crawl along on
> > horizontal surfaces, their hind legs are so twisted, it really looks
> > like their knees bend the wrong way.  [Reminds me of another recent
> > s.b.p. thread.]

[snip]

> >>>>> But theropod dinosaurs, from which birds are
> >>>>> supposed to have evolved, including velociraptors and Archaeopteryx,
> >>>>> didn't have this limitation, but stood with their knees more-or-less
> >>>>> straight, a very unavian posture.
>
> >>>> Which apparently demonstrates conclusively that Archaeopteryx is not a
> >>>> bird.
>
> >>> I take it you are being ironic here.
>
> >> Good catch.

[snip]

> >  You keep harping on the fact that even what looks like
> > direct ancestry from fossils could easily be falsified with more
> > complete data.
>
> You misunderstand. Nothing "looks like direct ancestry". There is no
> such "showing".

A complete lack of autapomorphies doesn't look like direct ancestry?
Is that because you are morally certain that autapomorphies will
eventually be discovered?

> >> It isn't lack
> >> of a complete specimen that's the problem. Now in fact Archaeopteryx has
> >> autapomorphies that argue against it being the ancestor.

[snip]

> >>> Nor
> >>> is it to say that it is a candidate for the *last* common ancestor--it
> >>> clearly is not.
>
> >> Well, I'm glad that's settled.
>
> > Are you ironically implying that it still hasn't been ruled out as the
> > LCA?
>
> No. I'm expressing annoyance regarding your tendency to ruminate to
> yourself in public. This is ruminating to yourself because the question
> is of concern and relevance only to you.
>
> > Bad catch this time, I fear.
>
> Did you catch the ironic intent of "good catch"?

No. Are you suggesting that my observation was just too trivial to be
worth posting here? How about if this thread had been crossposted to
talk.origins, where some participants (especially creationists) might
not know you were being ironic?

Peter Nyikos

[pnyikos]

On Oct 8, 4:54 pm, jillery <69jpi...@gmail.com> wrote:
> On Sat, 06 Oct 2012 08:25:17 -0700, John Harshman
>
>
>
>
>
> <jharsh...@pacbell.net> wrote:
> >On 10/6/12 4:17 AM, jillery wrote:
> >> On Fri, 05 Oct 2012 16:38:37 -0700, John Harshman

> >> <jharsh...@pacbell.net>  wrote:

Jillery doesn't think I deserve an apology over being repeatedly
slandered by certain buddies of hers/his, so why does [s]he even
bother writing "over this" and writing "an apology" instead of "any
apologies"?

Peter Nyikos

[John Harshman]

On 10/10/12 9:30 PM, pnyikos wrote:
> On Oct 5, 7:38 pm, John Harshman<jharsh...@pacbell.net> wrote:
>> On 10/5/12 10:38 AM, pnyikos wrote:
>>
>>> On Sep 29, 12:50 am, John Harshman<jharsh...@pacbell.net> wrote:
>>>> On 9/28/12 8:01 PM, pnyikos wrote:
>>
>>>>> On Sep 21, 11:36 am, John Harshman<jharsh...@pacbell.net> wrote:
>>>>>> jillery wrote:
>>
>>>>>>> <http://www.sciencedaily.com/releases/2009/06/090609092055.htm>
>>
>>>>>>> I freely admit most of this is new to me, that when birds walk,
>>>>>>> they hold their hips more or less in place while rotating
>>>>>>> their knees over a large angle.
>>
>>>>>> What you mean is that the femur rotates through a small angle and the
>>>>>> tibiotarsus through a large angle. And that's correct, for all birds.
>>
>>> It seems pretty clear from the linked article that this is NOT what
>>> the linked article meant, and so jillery probably did not mean it
>>> either. The picture accompanying the linked article labeled both the
>>> hip and the knee joints, using colors to highlight them.
>>
>> I fail to see how a hip joint can move. And the knee joint moves exactly
>> to the extent that the femur does.
>
> Yeah, but jillery didn't use the word "moving" but rather "rotating"
> in connection with the knee joint.

Why should it matter what words jillery used? What should matter is what
happens. What article meant, and what jillery presumably meant based on
the article, was what I said.

>> Anyway, you misunderstand the intent
>> of the diagram, which appears to be merely to locate the joints. It
>> should be clear from the text that "movement around the hip joint" means
>> "movement of the femur",
>
> Yes.
>
>> "movement around the knee joint means "movement
>> of the tibiotarsus",
>
> Not if the femur is also moving. Then the tibiotarsus has two things
> contributing to its movement, the other being the rotation of the knee
> joint.
>
> Oops, you'll claim this is a pointless exception that does nothing to
> advance the discussion [as below], won't you?

Depends. What exactly do you mean by "rotation of the knee joint"? If
you mean "movement of the distal end of the femur", then that's the only
thing contributing to movement of the knee joint. We have to separate
movement of the knee joint from movement around the knee joint, which
are two entirely separate things. Movement *of* the knee joint (i.e.
movement of the femur) contributes only a small amount to movement of
the leg. Movement *around* the knee joint contributes a much greater
amount. Don't confuse the two.

>> and "movement around the ankle joint" means
>> "movement of the tarsometatarsus".
>
> No comment.
>
>> "Movement of the joint" is quite
>> different from "movement around the joint".
>
> Oh, wait! suddenly YOU are talking about the pointless exception of
> the knee moving because the femur is moving, and not about the
> movement around the knee.

No, I'm talking about the difference between the two.

>> A bird's knee moves very
>> little, because the femur moves very little. A bird's ankle moves quite
>> a lot, because the tibiotarsus moves quite a lot. Is that clear now?
>
> The only unclear thing is whether you'll go childish and smart-alecky
> on account of my writing, "Not if the femur is also moving...."

Is explaining why you're wrong to conflate the two "childish and
smart-alecky"?

>>> By the way, when you said "rotates" did you mean around the long
>>> axis? I don't think you did, but that illustrates how the article
>>> and jillery were unambiguous, while you were not.
>>
>> As is so often the case, you have difficulty interpreting simple
>> statements. The usual technical term is "excursion". But yes, I meant
>> around the long axis.
>
> I'd call that twisting, not rotating. The long axis runs along the
> length of the bone, the way we mathematicians use the words "long
> axis".

Oops, sorry. I didn't mean that. This time I misunderstood you. I meant
movement *of* the long axis in approximately a parasagittal plane. You
know, what we normally think of as a walking motion.

>>> Yeah, I was really surprised to see that birds fuse THREE metatarsals;
>>> I'd only heard about cannon bones of camelids and some deer (not
>>> horses, where there is only one metatarsal besides the narrow splints)
>>> before, and those only fuse two.
>>
>>> Spurred by this article, I did some browsing in Romer's _Vertebrate
>>> Paleontology_ and saw that ornithomimids also fused three metatarsals,
>>> strengthening the case for birds being (descended from) dinosaurs.
>>
>> Not really, since the fusion was entirely convergent.
>
> Did the other maniraptorans have it?

Most did not. Think of Tyrannosaurus, for example. Archaeopteryx also,
as far as I recall, has no metatarsal fusion. It's a later development
in birds.

No. But there is no reason to suppose that a lack of skeletal
apomorphies shows a lack of divergence in other characters, even if only
genetic ones. A lack of apomorphies merely fails to argue against
ancestry, just as a photo of a lightless room fails to argue about the
presence of an elephant. Does a lightless room look like an elephant?

>>>> It isn't lack
>>>> of a complete specimen that's the problem. Now in fact Archaeopteryx has
>>>> autapomorphies that argue against it being the ancestor.
>
> [snip]
>
>
>>>>> Nor
>>>>> is it to say that it is a candidate for the *last* common ancestor--it
>>>>> clearly is not.
>>
>>>> Well, I'm glad that's settled.
>>
>>> Are you ironically implying that it still hasn't been ruled out as the
>>> LCA?
>>
>> No. I'm expressing annoyance regarding your tendency to ruminate to
>> yourself in public. This is ruminating to yourself because the question
>> is of concern and relevance only to you.
>>
>>> Bad catch this time, I fear.
>>
>> Did you catch the ironic intent of "good catch"?
>
> No. Are you suggesting that my observation was just too trivial to be
> worth posting here?

Yes. Good catch.

> How about if this thread had been crossposted to
> talk.origins, where some participants (especially creationists) might
> not know you were being ironic?

Still yes.

[pnyikos]

Revisiting a Science Daily article jillery posted about to
sci.bio.paleontology, I am struck by some strange language in it,
which might lead an unsophisticated reader to think that John Ruben
and Devon Quick, on the faculty of Oregon State University, had
serious doubts about common descent of tetrapods, let alone all
animals, let alone all life:

"We aren't suggesting that dinosaurs
and birds may not have had a common
ancestor somewhere in the distant past,"
Quick said. "That's quite possible and
is routinely found in evolution."
http://www.sciencedaily.com/releases/2009/06/090609092055.htm

But as several people, especially John Harshman, know, Ruben only
denies that birds are descended from dinosaurs. As an old-fashioned
systematist would say, he believes they are descended from thecodonts,
and Quick probably believes this too. Now that this old-fashioned
language has been "discredited," awkward language such as the above
can be found all over the place.

Most of the article is about respiration in birds, and has Ruben and
Quick on a soapbox about their pet theory.

Back in sci.bio.paleontology, the discussion centered on certain
features of avian leg movement that enable deeper breathing by them.

On Oct 11, 11:20 am, John Harshman <jharsh...@pacbell.net> wrote:
> On 10/10/12 9:30 PM, pnyikos wrote:
> > On Oct 5, 7:38 pm, John Harshman<jharsh...@pacbell.net>  wrote:
> >> On 10/5/12 10:38 AM, pnyikos wrote:
>
> >>> On Sep 29, 12:50 am, John Harshman<jharsh...@pacbell.net>    wrote:
> >>>> On 9/28/12 8:01 PM, pnyikos wrote:
>
> >>>>> On Sep 21, 11:36 am, John Harshman<jharsh...@pacbell.net>      wrote:
> >>>>>> jillery wrote:

> >>>>>>> I freely admit most of this is new to me, that when birds walk,
> >>>>>>> they hold their hips more or less in place while rotating
> >>>>>>>    their knees over a large angle.
>
> >>>>>> What you mean is that the femur rotates through a small angle and the
> >>>>>> tibiotarsus through a large angle. And that's correct, for all birds.
>
> >>> It seems pretty clear from the linked article that this is NOT what
> >>> the linked article meant, and so jillery probably did not mean it
> >>> either.  The picture accompanying the linked article labeled both the
> >>> hip and the knee joints, using colors to highlight them.
>
> >> I fail to see how a hip joint can move. And the knee joint moves exactly
> >> to the extent that the femur does.
>
> > Yeah, but jillery didn't use the word "moving" but rather "rotating"
> > in connection with the knee joint.
>
> Why should it matter what words jillery used? What should matter is what
> happens. What article meant, and what jillery presumably meant based on
> the article, was what I said.

Perhaps what you write is synonymous with what the article said, but
its actual words the article uses start out closer to those of jillery
than to yours:

During walking and running in birds,
hindlimb movement is generated primarily
at the knee and ankle joints; in humans,
movement occurs at the knee, ankle and hip joints.

Only the last part of the caption says what you do, and only half of
it, and it seems clear that this all is due to the lack of mobility in
the hip joint:

The bird's thigh does not move substantially
from its nearly horizontal position where it
provides rigid lateral support to the thin walled
air-sacs of the respiratory system.

[snip of mostly s.b.p. shop talk, some of which will be replied to
there in a few minutes]

> >>>>>>>   But theropod dinosaurs, from which birds are
> >>>>>>> supposed to have evolved, including velociraptors and Archaeopteryx,
> >>>>>>> didn't have this limitation, but stood with their knees more-or-less
> >>>>>>> straight, a very unavian posture.
>
> >>>>>> Which apparently demonstrates conclusively that Archaeopteryx is not a
> >>>>>> bird.
>
> >>>>> I take it you are being ironic here.
>
> >>>> Good catch.
>
> > [snip]

[snip of mostly s.b.p. shop talk]

> >> Did you catch the ironic intent of "good catch"?
>
> > No.  Are you suggesting that my observation was just too trivial to be
> > worth posting here?
>
> Yes. Good catch.

I suspect that you mean it this time.

> > How about if this thread had been crossposted to
> > talk.origins, where some participants (especially creationists) might
> > not know you were being ironic?
>
> Still yes.

Well, I've crossposted this to talk.origins. Let's see whether the
folks over there agree.

Peter Nyikos

[pnyikos]

On Oct 11, 11:20 am, John Harshman <jharsh...@pacbell.net> wrote:
> On 10/10/12 9:30 PM, pnyikos wrote:
> > On Oct 5, 7:38 pm, John Harshman<jharsh...@pacbell.net> wrote:
> >> On 10/5/12 10:38 AM, pnyikos wrote:
>
> >>> On Sep 29, 12:50 am, John Harshman<jharsh...@pacbell.net> wrote:
> >>>> On 9/28/12 8:01 PM, pnyikos wrote:
>
> >>>>> On Sep 21, 11:36 am, John Harshman<jharsh...@pacbell.net> wrote:
> >>>>>> jillery wrote:
> >>>>>>> <http://www.sciencedaily.com/releases/2009/06/090609092055.htm>
>
> >>>>>>> I freely admit most of this is new to me, that when birds walk,
> >>>>>>> they hold their hips more or less in place while rotating
> >>>>>>> their knees over a large angle.
>
> >>>>>> What you mean is that the femur rotates through a small angle and the
> >>>>>> tibiotarsus through a large angle. And that's correct, for all birds.
>
> >>> It seems pretty clear from the linked article that this is NOT what
> >>> the linked article meant, and so jillery probably did not mean it
> >>> either. The picture accompanying the linked article labeled both the
> >>> hip and the knee joints, using colors to highlight them.

[snip things addressed in my first reply]

> >> Anyway, you misunderstand the intent
> >> of the diagram, which appears to be merely to locate the joints. It
> >> should be clear from the text that "movement around the hip joint" means
> >> "movement of the femur",
>
> > Yes.

However, a better way of saying it is that range of movement of the
femur is *dependent* on mobility of the hip joint.

> >> "movement around the knee joint means "movement
> >> of the tibiotarsus",
>
> > Not if the femur is also moving. Then the tibiotarsus has two things
> > contributing to its movement, the other being the rotation of the knee
> > joint.
>
> > Oops, you'll claim this is a pointless exception that does nothing to
> > advance the discussion [as below], won't you?
>
> Depends. What exactly do you mean by "rotation of the knee joint"? If
> you mean "movement of the distal end of the femur", then that's the only
> thing contributing to movement of the knee joint.

That is not what I mean. As I sit here in my chair, my thigh is
immobile, and yet I can kick with my feet because my knee joints are
free to rotate. This rotation is effected by muscles that contract,
moving my tibia (and maybe fibula) through a wide arc.

That's the way I use "rotate". From what you say below, I might have
conveyed my thoughts better to you if I had said "rotation around the
knee joint" rather than just "rotation of the knee joint."

> We have to separate
> movement of the knee joint from movement around the knee joint, which
> are two entirely separate things. Movement *of* the knee joint (i.e.
> movement of the femur) contributes only a small amount to movement of
> the leg. Movement *around* the knee joint contributes a much greater
> amount. Don't confuse the two.

I never did. And I hope my (and maybe jillery's) use of "rotating"
won't cause you any more problems.

>
> >> and "movement around the ankle joint" means
> >> "movement of the tarsometatarsus".
>
> > No comment.
>
> >> "Movement of the joint" is quite
> >> different from "movement around the joint".
>
> > Oh, wait! suddenly YOU are talking about the pointless exception of
> > the knee moving because the femur is moving, and not about the
> > movement around the knee.
>
> No, I'm talking about the difference between the two.

Why even bring the "movement of the joint" into the picture? That
talks about change of location, not anything to do with what either
the article, or jillery, or I talked about.

[snip]

> >>> By the way, when you said "rotates" did you mean around the long
> >>> axis?    I don't think you did, but that illustrates how the article
> >>> and jillery were unambiguous, while you were not.
>
> >> As is so often the case, you have difficulty interpreting simple
> >> statements. The usual technical term is "excursion". But yes, I meant
> >> around the long axis.
>
> > I'd call that twisting, not rotating.  The long axis runs along the
> > length of the bone, the way we mathematicians use the words "long
> > axis".
>
> Oops, sorry. I didn't mean that. This time I misunderstood you. I meant
> movement *of* the long axis in approximately a parasagittal plane. You
> know, what we normally think of as a walking motion.

Well, I'm glad we cleared that up. Hope we cleared the part about
"rotation" up this time.

Peter Nyikos

[John Harshman]

On 10/11/12 7:49 PM, pnyikos wrote:
> Revisiting a Science Daily article jillery posted about to
> sci.bio.paleontology, I am struck by some strange language in it,
> which might lead an unsophisticated reader to think that John Ruben
> and Devon Quick, on the faculty of Oregon State University, had
> serious doubts about common descent of tetrapods, let alone all
> animals, let alone all life:
>
> "We aren't suggesting that dinosaurs
> and birds may not have had a common
> ancestor somewhere in the distant past,"
> Quick said. "That's quite possible and
> is routinely found in evolution."
> http://www.sciencedaily.com/releases/2009/06/090609092055.htm
>
> But as several people, especially John Harshman, know, Ruben only
> denies that birds are descended from dinosaurs.

Why "especially"?

> As an old-fashioned
> systematist would say, he believes they are descended from thecodonts,
> and Quick probably believes this too.

Actually, Ruben never really says what he thinks. Dunno about Quick.

> Now that this old-fashioned
> language has been "discredited," awkward language such as the above
> can be found all over the place.

Please. Don't blame poor writing on cladistics.

Only if you misunderstand what that sentence says, perhaps by
interpreting "at" to mean "by". To be excruciatingly clear: movement is
generated at a joint (at least the joints we're talking about) by
rotation in a parasagittal plane of the distal element. Movement at the
hip is movement of the femur; movement at the knee is movement of the
tibiotarsus; movement at the ankle is movement of the tarsometatarsus.
Ruben and Quick say exactly this, if you have the sense to read what
they say.

> Only the last part of the caption says what you do, and only half of
> it, and it seems clear that this all is due to the lack of mobility in
> the hip joint:
>
> The bird's thigh does not move substantially
> from its nearly horizontal position where it
> provides rigid lateral support to the thin walled
> air-sacs of the respiratory system.

I have no idea what you intend "lack of mobility in the hip joint" to
mean. I'm not sure you know what you mean, or what your point is.

> [snip of mostly s.b.p. shop talk, some of which will be replied to
> there in a few minutes]
>
>>>>>>>>> But theropod dinosaurs, from which birds are
>>>>>>>>> supposed to have evolved, including velociraptors and Archaeopteryx,
>>>>>>>>> didn't have this limitation, but stood with their knees more-or-less
>>>>>>>>> straight, a very unavian posture.
>>
>>>>>>>> Which apparently demonstrates conclusively that Archaeopteryx is not a
>>>>>>>> bird.
>>
>>>>>>> I take it you are being ironic here.
>>
>>>>>> Good catch.
>>
>>> [snip]
>
> [snip of mostly s.b.p. shop talk]
>
>>>> Did you catch the ironic intent of "good catch"?
>>
>>> No. Are you suggesting that my observation was just too trivial to be
>>> worth posting here?
>>
>> Yes. Good catch.
>
> I suspect that you mean it this time.

Your suspicions, as so often, are not warranted.

>>> How about if this thread had been crossposted to
>>> talk.origins, where some participants (especially creationists) might
>>> not know you were being ironic?
>>
>> Still yes.
>
> Well, I've crossposted this to talk.origins. Let's see whether the
> folks over there agree.

Agree with what? I don't really understand why you're posting this.

[John Harshman]

That would depend on what "mobility of the hip joint" means. But I don't
consider that a better way at all.

>>>> "movement around the knee joint means "movement
>>>> of the tibiotarsus",
>>
>>> Not if the femur is also moving. Then the tibiotarsus has two things
>>> contributing to its movement, the other being the rotation of the knee
>>> joint.
>>
>>> Oops, you'll claim this is a pointless exception that does nothing to
>>> advance the discussion [as below], won't you?
>>
>> Depends. What exactly do you mean by "rotation of the knee joint"? If
>> you mean "movement of the distal end of the femur", then that's the only
>> thing contributing to movement of the knee joint.
>
> That is not what I mean. As I sit here in my chair, my thigh is
> immobile, and yet I can kick with my feet because my knee joints are
> free to rotate. This rotation is effected by muscles that contract,
> moving my tibia (and maybe fibula) through a wide arc.

No, the joint isn't rotating. Your tibia and fibula are rotating. The
joint is in fact stationary. If you can move your tibia in a wide arc
without moving your fibula in a very similar arc, you have a very
unusual anatomy.

> That's the way I use "rotate". From what you say below, I might have
> conveyed my thoughts better to you if I had said "rotation around the
> knee joint" rather than just "rotation of the knee joint."

Exactly. The two mean quite different things.

>> We have to separate
>> movement of the knee joint from movement around the knee joint, which
>> are two entirely separate things. Movement *of* the knee joint (i.e.
>> movement of the femur) contributes only a small amount to movement of
>> the leg. Movement *around* the knee joint contributes a much greater
>> amount. Don't confuse the two.
>
> I never did. And I hope my (and maybe jillery's) use of "rotating"
> won't cause you any more problems.

If you didn't confuse the two, what are we arguing about? What in fact
do you think the linked article meant?

>>>> and "movement around the ankle joint" means
>>>> "movement of the tarsometatarsus".
>>
>>> No comment.
>>
>>>> "Movement of the joint" is quite
>>>> different from "movement around the joint".
>>
>>> Oh, wait! suddenly YOU are talking about the pointless exception of
>>> the knee moving because the femur is moving, and not about the
>>> movement around the knee.
>>
>> No, I'm talking about the difference between the two.
>
> Why even bring the "movement of the joint" into the picture? That
> talks about change of location, not anything to do with what either
> the article, or jillery, or I talked about.

"Movement of the joint" is what you said. If that isn't what you meant,
what is our disagreement?

>>>>> By the way, when you said "rotates" did you mean around the long
>>>>> axis? I don't think you did, but that illustrates how the article
>>>>> and jillery were unambiguous, while you were not.
>>
>>>> As is so often the case, you have difficulty interpreting simple
>>>> statements. The usual technical term is "excursion". But yes, I meant
>>>> around the long axis.
>>
>>> I'd call that twisting, not rotating. The long axis runs along the
>>> length of the bone, the way we mathematicians use the words "long
>>> axis".
>>
>> Oops, sorry. I didn't mean that. This time I misunderstood you. I meant
>> movement *of* the long axis in approximately a parasagittal plane. You
>> know, what we normally think of as a walking motion.
>
> Well, I'm glad we cleared that up. Hope we cleared the part about
> "rotation" up this time.

What was the point of your initial post? Did you have one?

[J.J. O'Shea]

On Thu, 11 Oct 2012 23:25:51 -0400, John Harshman wrote
(in article <OZKdnWTMUfZ...@giganews.com>):

Well, Peter N _is_ the leading expert at arguing from false premises.

>
>> Only the last part of the caption says what you do, and only half of
>> it, and it seems clear that this all is due to the lack of mobility in
>> the hip joint:
>>
>> The bird's thigh does not move substantially
>> from its nearly horizontal position where it
>> provides rigid lateral support to the thin walled
>> air-sacs of the respiratory system.
>
> I have no idea what you intend "lack of mobility in the hip joint" to
> mean. I'm not sure you know what you mean, or what your point is.

His only point is to mount an unwarranted attack on someone much more honest
than he is.

>
>> [snip of mostly s.b.p. shop talk, some of which will be replied to
>> there in a few minutes]
>>
>>>>>>>>>> But theropod dinosaurs, from which birds are
>>>>>>>>>> supposed to have evolved, including velociraptors and Archaeopteryx,
>>>>>>>>>> didn't have this limitation, but stood with their knees more-or-less
>>>>>>>>>> straight, a very unavian posture.
>>>
>>>>>>>>> Which apparently demonstrates conclusively that Archaeopteryx is not
>>>>>>>>> a
>>>>>>>>> bird.
>>>
>>>>>>>> I take it you are being ironic here.
>>>
>>>>>>> Good catch.
>>>
>>>> [snip]
>>
>> [snip of mostly s.b.p. shop talk]
>>
>>>>> Did you catch the ironic intent of "good catch"?
>>>
>>>> No. Are you suggesting that my observation was just too trivial to be
>>>> worth posting here?
>>>
>>> Yes. Good catch.
>>
>> I suspect that you mean it this time.
>
> Your suspicions, as so often, are not warranted.

Of course not.

>
>>>> How about if this thread had been crossposted to
>>>> talk.origins, where some participants (especially creationists) might
>>>> not know you were being ironic?
>>>
>>> Still yes.
>>
>> Well, I've crossposted this to talk.origins. Let's see whether the
>> folks over there agree.
>
> Agree with what? I don't really understand why you're posting this.
>

Oh, that's clear enough. The Lord of Liars is attempting to open a second
front on his assault on jillery, and is doing as well as could be expected,
given his limitations.

--
email to oshea dot j dot j at gmail dot com.

[jillery]

Yeppers. The entire topic was thoroughly discussed and settled before
Rockhead tossed in his two bits. From that, it has devolved into
meaningless asides and irrelevant pedantic quibbling, a characteristic
common among topics featuring his participation.

[J.J. O'Shea]

On Fri, 12 Oct 2012 14:42:07 -0400, jillery wrote
(in article <v2pg781ksf5ngdf87...@4ax.com>):

Does he _never_ tire of showing the world exactly what a slime he is?

[Augray]

On Oct 11, 11:20 am, John Harshman <jharsh...@pacbell.net> wrote:

[big snip]

> Archaeopteryx also,
> as far as I recall, has no metatarsal fusion. It's a later development
> in birds.

If I recall correctly, different specimens show different degrees of
fusion, from none to partial. Some speculate that the degree of fusion
is a function of ontogeny.

[snip the rest]

[John Harshman]

Does it disturb you at all that you seem like a stalker?

[Richard Norman]

It certainly disturbs others -- me, for instance.

[drose...@yahoo.com]

On Friday, September 21, 2012 7:59:23 AM UTC-4, jillery wrote:
> Perhaps this newsgroup is a better place to discuss this after all.
>
>
>

> I ran across these ScienceDaily articles:
>
>
>
> <http://www.sciencedaily.com/releases/2010/02/100209183335.htm>
>
>
>
> birds are not evolved from dinosaurs, but that some dinosaurs may be
>
> evolved from birds, and:
>
>
>
> <http://www.sciencedaily.com/releases/2009/06/090609092055.htm>
>
>
>
> extant birds hold their femurs semi-horizontally, to support their
>
> internal air sacs, while apparently theropod dinosaurs did not, making
>
> it unlikely birds arose from theropod dinosaurs.
>
>
>
> The above is based on the following research report:
>
>
>
> <http://onlinelibrary.wiley.com/doi/10.1002/jmor.10752/pdf>
>
>
>
>
>
> Contrasting with the above, I found this:
>
>
>
> <http://www.sciencedaily.com/releases/2007/11/071107074326.htm>
>
>
>
> breathing structures, known as uncinate processes, are also present in
>
> maniraptoran dinosaurs and Archaeopteryx.
>
>
>
> The above is based on the following research report:
>
>
>
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596187/

>
>
>
> I freely admit most of this is new to me, that when birds walk, they
>
> hold their hips more or less in place while rotating their knees over
>

> a large angle. In contrast, most mammals move their hips over a much
>
> larger angle than do birds, even nonflying birds. Apparently even

>
> penguins stand in a kind of squat, with their thighs close to the
>
> abdomen and their knees bent.
>
>
>
> According to Quick and Ruben, this adaptation is necessary in order to
>
> support the posterior air sac during inspiration, that auxiliary
>
> structures like gastralia and uncinate processes don't prevent its
>

> paradoxical collapse. But theropod dinosaurs, from which birds are

>
> supposed to have evolved, including velociraptors and Archaeopteryx,
>
> didn't have this limitation, but stood with their knees more-or-less
>
> straight, a very unavian posture.
>
>
>

> So, assuming the above anatomical statements are correct, does that
>
> necessarily mean birds did not evolve from dinosaurs? Or that some
>
> dinosaurs evolved from birds? Isn't it plausible that this anatomical
>
> requirement became necessary after birds evolved powered flight? Is
>
> this a big question in the scientific community?

I am not a professional paleontologist. However, I have heard a few paleontologists talk on this. I don't have articles to reference. However, what I heard was this.
Almost surely, the basics of the avian respiratory system evolved before the birds evolved flight. The metabolic efficiency of the avian respiratory system would be just as useful for an animal running after it prey as for flying. The skeletons of some theropods, not all, are consistent with an avian type respiratory system.
The dinosaurs are unlikely to have developed the precise same respiratory system as birds, as they have different lifestyles. However, dinosaurs have a lot of the prerequisites for system like an avian system.
Most dinosaurs had hollow bones filled with air. The air filled bones served in a number of ways. For instance, it lightened the bones in the larger dinosaurs. Large dinosaurs had bones that were reinforced at the joints where most of the stresses occurred. The hollow bones probably helped some dinosaurs swim through the buoyancy.
The ancestors of the dinosaurs, such as thecondonts, were probably had to live in the water. That may be where the hollow bones first evolved. However, other features probably evolved later that took advantage of the hollow bones. Like many things in evolution, the different parts of the system may have evolved piecemeal but came together later for larger system. By the late Jurrassic, birds and thecodonts are barely distinguishable. It is very difficult to distinguish them.
There was always, from the beginning of dinosaur studies, this controversy as to whether dinosaurs were reptiles or birds. The fused clavicle, otherwise called the wishbone, was present in a few species of theropods.The absence of wishbones among dinosaur fossils was crucial in 1936 for the decision to classify dinosaurs as reptiles. However, dinosaur skeletons with wishbones were discovered in 1940. Many theropods were discovered to have wishbones. There was a recent discovery that dinosaurs had some dinosaurs had feathers and some had quills. The quills are important because they are not scales. The feather did not evolved directly from a scale, it evolved from quills.
I don't know how your sources know that femurs have to be held horizontally to protect the air sacs. I don't know how your sources know that dinosaurs didn't hold their femurs horizontally. I do know that there were to orders of dinosaurs which held their femurs differently. I suspect that your sources may be pointing at one group of dinosaurs that are more distantly related to birds than the other group.
There was not only more diversity among dinosaurs in the Mesozoic, there was more diversity among birds. I doubt that all dinosaurs, or even all birds, had the same type of respiratory system.
My main problem is picturing what you mean by "air sacs collapsing". Furthermore, I don't know where in the dinosaurs body the air sacs were. Maybe the air sacs were in the forearms, which were generally held horizontally.
I am not saying that you are wrong in what you are saying. I am saying that I never heard the claim that dinosaurs were that different from birds that they could never use air sacs in their bodies the way birds use air sacs.
BTW: The museums in New Mexico there also like to show models of the road runner next to models of the Rioaribosaurus (previously, Coelophysis), their state dinosaur. Road runners are all over the state, so one could at least verify that their models of road runners was accurate.
The stance of the two animals was very similar, at least the way these museum showed it. There didn't seem to be a significant difference in the way the road runner runs and the Rioaribosaurus ran. Rioaribosaurus had a more substantial tail, of course. However, both were very predators.
Road runners are a little more aggressive than is shown in the cartoon. These guys hunt rattlesnakes for lunch. They fly a little (like chickens) but their main hunting techniques involve fast motions on the ground. They fly only to get away from enemies. This is one technique you never see used on coyote.
It seems to me that road runner femurs aren't quite horizontal as you say. However, I may be wrong.