Were there any avian dinosaurs with horns

[Metspitzer]

It wasn't a trick question it was just a typo.

Also, were there any avian dinosaurs that walked on four legs?

[Richard Norman]

On Fri, 13 Jan 2012 14:17:32 -0500, Metspitzer <kilo...@charter.net>
wrote:

>It wasn't a trick question it was just a typo.
>
>Also, were there any avian dinosaurs that walked on four legs?

What do you mean by "avian dinosaur"?

[Arkalen]

(2012/01/14 4:17), Metspitzer wrote:
> It wasn't a trick question it was just a typo.
>
> Also, were there any avian dinosaurs that walked on four legs?
>

Don't all avian dinosaurs have wings ? It would depend on which
dinosaurs are "avian". If they include dinosaurs with wings that still
have claws and all that stuff like Archaeopteryx, then theoretically I
suppose a secondarily flightless dinosaur in that group could have
walked on four legs. I don't think we know of any such dinosaur.

--
Arkalen
Praise be to magic Woody-Allen zombie superhero telepathic vampire
quantum hovercraft Tim! Jesus.

[Richard Norman]

On Sat, 14 Jan 2012 04:43:06 +0900, Arkalen <ark...@inbox.com> wrote:

>(2012/01/14 4:17), Metspitzer wrote:
>> It wasn't a trick question it was just a typo.
>>
>> Also, were there any avian dinosaurs that walked on four legs?
>>
>
>Don't all avian dinosaurs have wings ? It would depend on which
>dinosaurs are "avian". If they include dinosaurs with wings that still
>have claws and all that stuff like Archaeopteryx, then theoretically I
>suppose a secondarily flightless dinosaur in that group could have
>walked on four legs. I don't think we know of any such dinosaur.

Microraptor had "wings" on all four legs. How it walked is another
story.

Wikipedia says that the Coelurosauria, "the clade containing all
theropod dinosaurs more closely related to birds than to carnosaurs"
were all bipedal.

John Harshman, our resident authority on all these matters, may have
better information that differs.

[John Harshman]

Metspitzer wrote:
> It wasn't a trick question it was just a typo.

Then the answer is no, depending on what you mean by "horns". If you
want to call the big block of ivory sticking out of the heads of some
species of hornbill a horn, then yes. Or the spongy thing on a horned
guan. Or any number of other bits I wouldn't count.

> Also, were there any avian dinosaurs that walked on four legs?

No. Though some scrambled about in trees using their forlimbs, juvenile
hoatzins do this today, for example. There is also a Caribbean fossil
ibis that was once proposed to be quadrupedal, but it probably wasn't.

[John Harshman]

"Bird"?

[John Harshman]

Arkalen wrote:
> (2012/01/14 4:17), Metspitzer wrote:
>> It wasn't a trick question it was just a typo.
>>
>> Also, were there any avian dinosaurs that walked on four legs?
>>
>
> Don't all avian dinosaurs have wings ? It would depend on which
> dinosaurs are "avian". If they include dinosaurs with wings that still
> have claws and all that stuff like Archaeopteryx, then theoretically I
> suppose a secondarily flightless dinosaur in that group could have
> walked on four legs. I don't think we know of any such dinosaur.
>

It's vaguely conceivable that some therizinosaurs were quadrupedal.

[pnyikos]

Here's another question for you: were pterosaurs bipedal or
quadrupedal?

And another: if bipedal, which two feet did they walk on?

In re the former question, John Ostrom's answer is "quadrupedal" but
back in the 1990's one of our resident paleontologists in s.b.p.
claimed they were bipedal.

Google seems to have dropped our exchange on that. As well as I
recall, I told him:

"For what it's worth, John Ostrom disagrees with you" and then I
quoted something from an article by Ostrom, giving a precise
reference.

"I am aware of the mild disagreement between John and myself..." was
about how he began.

In re the latter question: the South Carolina Museum, here in
Columbia, once hosted a traveling exhibit on the land vertebrates of
the Mesozoic, and one life-size exhibit was a model of Pteranodon
walking on its front feet, with the hind feet suspended in air.

A famous writer once did a science fiction story about a species in
the Galactic Federation (not sure that was what he called it) which
had an intelligent species of the same sort in it.

IIRC the author was Poul Anderson, and what I saw was a first
installment in a science fiction magazine, with a picture showing one
of the members of the species sitting at a bar, holding a drink with
one of its "hind hands".

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

[Arkalen]

You'd only call them "hind hands" as opposed to "hands" if there were
also "forehands". Sounds to me like that alien species is
chimpanzee-like more than anything. But you read the story, maybe they
specified in it that it was a creature with its back limbs as hands and
front limbs as feet.

Either way that sounds to me like a very unlikely combination, because
if you're going to have hands it's presumably to use them, and in that
case you'll want them to be close to where most of your sensory organs
are, i.e. the head.

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

[Alan]

"pnyikos" <nyi...@bellsouth.net> wrote in message
news:fb2610ae-5c50-4348...@24g2000yqi.googlegroups.com...

"Wings of Victory" and "Wingless in Avalon" part of the "Earthbook of
Stormgate" 1,2,3. And the Ythrians have feathers.

Alan

[jillery]

On Sat, 14 Jan 2012 04:43:06 +0900, Arkalen <ark...@inbox.com> wrote:

>(2012/01/14 4:17), Metspitzer wrote:
>> It wasn't a trick question it was just a typo.
>>
>> Also, were there any avian dinosaurs that walked on four legs?
>>
>
>Don't all avian dinosaurs have wings ? It would depend on which
>dinosaurs are "avian". If they include dinosaurs with wings that still
>have claws and all that stuff like Archaeopteryx, then theoretically I
>suppose a secondarily flightless dinosaur in that group could have
>walked on four legs. I don't think we know of any such dinosaur.

Hoatzin chicks have claws on their wings, which they use with
reasonable dexterity to climb up twigs. Once the wings are strong
enough to fly, the claws are lost.

[John Harshman]

pnyikos wrote:
> On Jan 13, 3:12 pm, John Harshman <jharsh...@pacbell.net> wrote:
>> Arkalen wrote:
>>> (2012/01/14 4:17), Metspitzer wrote:
>>>> It wasn't a trick question it was just a typo.
>>>> Also, were there any avian dinosaurs that walked on four legs?
>>> Don't all avian dinosaurs have wings ? It would depend on which
>>> dinosaurs are "avian". If they include dinosaurs with wings that still
>>> have claws and all that stuff like Archaeopteryx, then theoretically I
>>> suppose a secondarily flightless dinosaur in that group could have
>>> walked on four legs. I don't think we know of any such dinosaur.
>> It's vaguely conceivable that some therizinosaurs were quadrupedal.
>
> Here's another question for you: were pterosaurs bipedal or
> quadrupedal?

Current consensus is the latter.

> And another: if bipedal, which two feet did they walk on?

Are you seriously entertaining the idea of pterosaurs walking on their
hands? If so, you've been reading too much Poul Anderson.

> In re the former question, John Ostrom's answer is "quadrupedal" but
> back in the 1990's one of our resident paleontologists in s.b.p.
> claimed they were bipedal.

That was the claim advanced for some years by Kevin Padian. But no longer.

> Google seems to have dropped our exchange on that. As well as I
> recall, I told him:
>
> "For what it's worth, John Ostrom disagrees with you" and then I
> quoted something from an article by Ostrom, giving a precise
> reference.

Of course it's worth nothing. The reasons for disagreement are another
matter.

> "I am aware of the mild disagreement between John and myself..." was
> about how he began.
>
> In re the latter question: the South Carolina Museum, here in
> Columbia, once hosted a traveling exhibit on the land vertebrates of
> the Mesozoic, and one life-size exhibit was a model of Pteranodon
> walking on its front feet, with the hind feet suspended in air.

I would be interested to know where they got that idea.

> A famous writer once did a science fiction story about a species in
> the Galactic Federation (not sure that was what he called it)

He didn't call it anything, because you are misremembering that they
were part of such an entity.

> which
> had an intelligent species of the same sort in it.
>
> IIRC the author was Poul Anderson, and what I saw was a first
> installment in a science fiction magazine, with a picture showing one
> of the members of the species sitting at a bar, holding a drink with
> one of its "hind hands".

You're talking about the Ythri, part of his "Technic Civilization" universe.

[*Hemidactylus*]

"Ouch"! :-)


--
*Hemidactylus*
-Tebow doesn't need Patriots sideline video intel
*Atheists for Tebow over Belichick*

[John Harshman]

And various places in other stories too.

[Will in New Haven]

The Ythri. I always thought of them as using their hind legs as
manipulators and walking on the "elbows" of their forelimb-wings.
However, I didn't know about the picture in the magazine. It just
seemed logical.

--
Will in New Haven

[Will in New Haven]

On Jan 13, 7:05 pm, John Harshman <jharsh...@pacbell.net> wrote:
> pnyikos wrote:
> > On Jan 13, 3:12 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >> Arkalen wrote:
> >>> (2012/01/14 4:17), Metspitzer wrote:
> >>>> It wasn't a trick question it was just a typo.
> >>>> Also, were there any avian dinosaurs that walked on four legs?
> >>> Don't all avian dinosaurs have wings ? It would depend on which
> >>> dinosaurs are "avian". If they include dinosaurs with wings that still
> >>> have claws and all that stuff like Archaeopteryx, then theoretically I
> >>> suppose a secondarily flightless dinosaur in that group could have
> >>> walked on four legs. I don't think we know of any such dinosaur.
> >> It's vaguely conceivable that some therizinosaurs were quadrupedal.
>
> > Here's another question for you: were pterosaurs bipedal or
> > quadrupedal?
>
> Current consensus is the latter.
>
> > And another: if bipedal, which two feet did they walk on?
>
> Are you seriously entertaining the idea of pterosaurs walking on their
> hands? If so, you've been reading too much Poul Anderson.

Can't be done. I've read everything he wrote, including non-fiction.
Some of it wasn't as good as the rest but none of it was too much. And
there won't be anymore.

--
Will in New Haven


>

[John Harshman]

Will in New Haven wrote:
> On Jan 13, 7:05 pm, John Harshman <jharsh...@pacbell.net> wrote:
>> pnyikos wrote:
>>> On Jan 13, 3:12 pm, John Harshman <jharsh...@pacbell.net> wrote:
>>>> Arkalen wrote:
>>>>> (2012/01/14 4:17), Metspitzer wrote:
>>>>>> It wasn't a trick question it was just a typo.
>>>>>> Also, were there any avian dinosaurs that walked on four legs?
>>>>> Don't all avian dinosaurs have wings ? It would depend on which
>>>>> dinosaurs are "avian". If they include dinosaurs with wings that still
>>>>> have claws and all that stuff like Archaeopteryx, then theoretically I
>>>>> suppose a secondarily flightless dinosaur in that group could have
>>>>> walked on four legs. I don't think we know of any such dinosaur.
>>>> It's vaguely conceivable that some therizinosaurs were quadrupedal.
>>> Here's another question for you: were pterosaurs bipedal or
>>> quadrupedal?
>> Current consensus is the latter.
>>
>>> And another: if bipedal, which two feet did they walk on?
>> Are you seriously entertaining the idea of pterosaurs walking on their
>> hands? If so, you've been reading too much Poul Anderson.
>
> Can't be done. I've read everything he wrote, including non-fiction.
> Some of it wasn't as good as the rest but none of it was too much. And
> there won't be anymore.

Actually, I've read a couple of quite bad books by Anderson. One was
apparently a very early effort, and the other was an attempt at
"mainstream" fiction.

But I take your point.

[JennyB]

On Friday, 13 January 2012 22:12:01 UTC, Arkalen wrote:

> You'd only call them "hind hands" as opposed to "hands" if there were
> also "forehands". Sounds to me like that alien species is
> chimpanzee-like more than anything. But you read the story, maybe they
> specified in it that it was a creature with its back limbs as hands and
> front limbs as feet.
>
> Either way that sounds to me like a very unlikely combination, because
> if you're going to have hands it's presumably to use them, and in that
> case you'll want them to be close to where most of your sensory organs
> are, i.e. the head.
>

I've come across this pattern long ago in a coffee-table book (whose title I can't remember on speculative future evolution. In that case, the ancestors were flightless vampire bats.

[Ron O]

On Jan 13, 6:01 pm, jillery <69jpi...@gmail.com> wrote:

Check out your chicken wings. They have a short finger along with the
extended finger that makes up the wing tip. A lot of times this is
just a nub, but for some birds it can be over a centimeter in length
and have a nicely curved very sharp claw. There is a full range of
types between nub and finger with fully formed claw.

Ron Okimoto

[jillery]

Now there's an oranism with a very specialized niche.

[jillery]

On Sat, 14 Jan 2012 06:38:25 -0800 (PST), Ron O <roki...@cox.net>
wrote:

Is this the same thing as birds' alula?

[Arkalen]

Yeah. The thing is, there ARE animals that use their hind legs for
tool-using - namely, many birds. But the thing is, they ALSO use their
hind legs for walking. And all birds that become secondarily flightless
lose the use of their wings altogether; they seem to be too specialized
an organ to easily be exapted for a different complex task.

Now I could more easily see it with bats, because some of their wings
are less specialized than birds' (they have fingers and stuff). I can
also (although it's more difficult) see flying animals whose legs become
useless for walking. But if the wings are unspecialized enough to be
used for walking, they're unspecialized enough to be used for
tool-using, and if the legs are useless for walking I'd think they're
too useless for tool use as well.
In other words, I'd see a secondarily flightless bat that used its wings
for walking AND tool-using before I saw one that walked on its front
legs and manipulated things with its hind limbs.

Obviously this isn't much more than an argument from personal
incredulity, and science-fiction authors don't need to follow my
standards of biological plausibility to make up their aliens. I'm just
thinking aloud here.

Thinking aloud though, I was trying to think of any animals that use
their back limbs for tool use and I realize some DO exist - spiders for
example. Well, maybe I shouldn't say "tool use" and more "fine
manipulation", but I can imagine aliens that use their back limbs for
tool use evolving from spider-like ancestors. Are there any tetrapod
examples of something like this at all ?

[John Harshman]

No. The allula is the part of the bird's wing attached to the thumb, not
the thumb itself. Many birds have short claws on their thumbs, and some
on the first finger too. Though very few make as much use of them as
young hoatzins do.

See this:
http://scienceblogs.com/tetrapodzoology/2010/06/clubs_spurs_spikes_and_claws.php

[Richard Norman]

On Sat, 14 Jan 2012 09:48:24 -0500, jillery <69jp...@gmail.com>
wrote:

In Algeria it is sort of common.

[jillery]

Pedantic point, it's not a thumb:

http://scienceblogs.com/pharyngula/2009/06/digit_numbering_and_limb_devel.php

More important question, I don't understand the distinction you're
trying to make. Are you suggesting birds' alula are passive
mechanisms? IIUC birds have direct control of when and how much to
extend it, typically just before landing. Is it not reasonable to
consider the control mechanism for the alula to be *part* of the
alula?

[jillery]

Yes, I'm guilty of the sin of oranism.

[John Harshman]

Pedant point: Yes it is. If the frame shift explanation is correct, it's
digit I. If the condensations are counted wrong (my favorite) it's digit
I. There is no reasonable sense in which it's digit II.

> More important question, I don't understand the distinction you're
> trying to make. Are you suggesting birds' alula are passive
> mechanisms?

No. What gave that impression?

> IIUC birds have direct control of when and how much to
> extend it, typically just before landing. Is it not reasonable to
> consider the control mechanism for the alula to be *part* of the
> alula?

Yes. But part of something isn't that same as that thing. So your
question had to be answered in the negative.

[jillery]

On Sat, 14 Jan 2012 20:01:32 -0800, John Harshman

Dueling authorities. I find PZ's embryological evidence and
explanation persuasive, and Darren Naish's demurral telling. But I
admit I am no expert, and so even my opinion of their opinions isn't
worth much.

>> More important question, I don't understand the distinction you're
>> trying to make. Are you suggesting birds' alula are passive
>> mechanisms?
>
>No. What gave that impression?

It is the only way I knew how make sense of what you wrote.

>> IIUC birds have direct control of when and how much to
>> extend it, typically just before landing. Is it not reasonable to
>> consider the control mechanism for the alula to be *part* of the
>> alula?
>
>Yes. But part of something isn't that same as that thing. So your
>question had to be answered in the negative.

So it *is* part of the alula. So is the part you mentioned. They are
both parts, not the whole. You made a false distinction.

[John Harshman]

PZ likes the frame shift, but I don't understand why a frame shift makes
it digit II. The point of a frame shift is that the former digit II
becomes digit I.

>>> More important question, I don't understand the distinction you're
>>> trying to make. Are you suggesting birds' alula are passive
>>> mechanisms?
>> No. What gave that impression?
>
> It is the only way I knew how make sense of what you wrote.

Then you need to find another way. I don't understand your interpretation.

>>> IIUC birds have direct control of when and how much to
>>> extend it, typically just before landing. Is it not reasonable to
>>> consider the control mechanism for the alula to be *part* of the
>>> alula?
>> Yes. But part of something isn't that same as that thing. So your
>> question had to be answered in the negative.
>
> So it *is* part of the alula. So is the part you mentioned. They are
> both parts, not the whole. You made a false distinction.

Not that I can see.

[Friar Broccoli]

So does digit IV become III? Or do we count 1, 2, 4 or something like
that?

>
>>>> More important question, I don't understand the distinction you're
>>>> trying to make. Are you suggesting birds' alula are passive
>>>> mechanisms?
>>> No. What gave that impression?
>>
>> It is the only way I knew how make sense of what you wrote.
>
> Then you need to find another way. I don't understand your interpretation.
>
>>>> IIUC birds have direct control of when and how much to
>>>> extend it, typically just before landing. Is it not reasonable to
>>>> consider the control mechanism for the alula to be *part* of the
>>>> alula?
>>> Yes. But part of something isn't that same as that thing. So your
>>> question had to be answered in the negative.
>>
>> So it *is* part of the alula. So is the part you mentioned. They are
>> both parts, not the whole. You made a false distinction.
>
> Not that I can see.
>

--
Friar Broccoli (Robert Keith Elias), Quebec Canada
I consider ALL arguments in support of my views

[jillery]

On Sun, 15 Jan 2012 06:56:56 -0800, John Harshman

PZ also likes to number bird digits as DII, DIII, and DIV. He does
not say in this article, but I infer he supports numbering dinosaur
digits that way also, to reflect their presumptive embryologic
origins. And IIUC Darren Nash, he is of the opinion that most
embryologists would agree with PZ, even though Nash does not.

IIUC the consequence of the frame shift is to change the "identity" of
the embryologic finger condensations. The argument is that initial
embryologic hand development sequence is pretty much the same for most
tetrapods. So CIV, the "ring" finger, necessarily develops first,
then CV, CIII, CII, and finally CI, the thumb, in that order. Birds
and presumably some dinosaurs, get their three digits by losing their
embryologic CI and CV. This is the rationale behind identifying bird
fingers as DII, DIII, and DIV. It's not a miscount; it's the same
numbering as what's used for your fingers.

But the actual digit identities of these condensations, what makes CI
a thumb etc, is established in a much later step. It's that step
which presumably frame-shifted, so that CII becomes DI, CIII becomes
DII, and CIV become DIII.

Like I said, it makes sense to me.

>>>> More important question, I don't understand the distinction you're
>>>> trying to make. Are you suggesting birds' alula are passive
>>>> mechanisms?
>>> No. What gave that impression?
>>
>> It is the only way I knew how make sense of what you wrote.
>
>Then you need to find another way. I don't understand your interpretation.

You asked a question. I answered it honestly. Only after I answered
did you say I was wrong, but I still don't understand the distinction
you're trying to make below.

>>>> IIUC birds have direct control of when and how much to
>>>> extend it, typically just before landing. Is it not reasonable to
>>>> consider the control mechanism for the alula to be *part* of the
>>>> alula?
>>> Yes. But part of something isn't that same as that thing. So your
>>> question had to be answered in the negative.
>>
>> So it *is* part of the alula. So is the part you mentioned. They are
>> both parts, not the whole. You made a false distinction.
>
>Not that I can see.

Let's try this. I stipulate for argument's sake birds' wings include
a thumb. You wrote above the thumb is part of an alula. This implies
there are *other* parts of an alula. That part of the wing you
identified as attached to the thumb is also *part* of an alula A
complete alula is the entire collection of all its parts. If you
remove any part, you no longer have a complete alula. I identified
*part* of an alula. You identified *part* of an alula. The part you
identified is no more a complete alula than is my part. Parts is
parts. Our statements are equivalent. You made a false distinction.

[Ernest Major]

In message <l0w*gA...@news.chiark.greenend.org.uk>, Arkalen
<ark...@inbox.com> writes

>Yeah. The thing is, there ARE animals that use their hind legs for
>tool-using - namely, many birds. But the thing is, they ALSO use their
>hind legs for walking. And all birds that become secondarily flightless
>lose the use of their wings altogether; they seem to be too specialized
>an organ to easily be exapted for a different complex task.

Counter-example to the latter - penguins. (Unless you want to consider
penguins as flying in water.)
--
alias Ernest Major

[John Harshman]

According to the frame shift hypothesis, I, II, III become II, III, IV.
The standard amniote phalangeal formula is 2-3-4-5-4. The standard
theropod formula is 2-3-4. You figure it.

[John Harshman]

Exactly. So if we're talking about digits rather than condensations,
birds have DI, DII, and DIII.

> Like I said, it makes sense to me.
>
>>>>> More important question, I don't understand the distinction you're
>>>>> trying to make. Are you suggesting birds' alula are passive
>>>>> mechanisms?
>>>> No. What gave that impression?
>>> It is the only way I knew how make sense of what you wrote.
>> Then you need to find another way. I don't understand your interpretation.
>
> You asked a question. I answered it honestly. Only after I answered
> did you say I was wrong, but I still don't understand the distinction
> you're trying to make below.

You're wrong about that too. I said you were wrong, and then asked what
made you think otherwise. The distinction is simple. The digit isn't the
allula. It's the skeletal portion of the allula.

>>>>> IIUC birds have direct control of when and how much to
>>>>> extend it, typically just before landing. Is it not reasonable to
>>>>> consider the control mechanism for the alula to be *part* of the
>>>>> alula?
>>>> Yes. But part of something isn't that same as that thing. So your
>>>> question had to be answered in the negative.
>>> So it *is* part of the alula. So is the part you mentioned. They are
>>> both parts, not the whole. You made a false distinction.
>> Not that I can see.
>
> Let's try this. I stipulate for argument's sake birds' wings include
> a thumb. You wrote above the thumb is part of an alula. This implies
> there are *other* parts of an alula. That part of the wing you
> identified as attached to the thumb is also *part* of an alula A
> complete alula is the entire collection of all its parts. If you
> remove any part, you no longer have a complete alula. I identified
> *part* of an alula. You identified *part* of an alula. The part you
> identified is no more a complete alula than is my part. Parts is
> parts. Our statements are equivalent. You made a false distinction.

Ah, I see what you mean. OK, what I said was wrong too. The allula is
the entire package. Now are we agreed on that point?

[Friar Broccoli]

.

> According to the frame shift hypothesis, I, II, III become II, III, IV.
> The standard amniote phalangeal formula is 2-3-4-5-4. The standard
> theropod formula is 2-3-4. You figure it.

I feel like an idiot. All I had to do was look:
http://scienceblogs.com/pharyngula/upload/2009/06/digit_frameshift.gif

>
>>>>>> More important question, I don't understand the distinction you're
>>>>>> trying to make. Are you suggesting birds' alula are passive
>>>>>> mechanisms?
>>>>> No. What gave that impression?
>>>>
>>>> It is the only way I knew how make sense of what you wrote.
>>>
>>> Then you need to find another way. I don't understand your
>>> interpretation.
>>>
>>>>>> IIUC birds have direct control of when and how much to
>>>>>> extend it, typically just before landing. Is it not reasonable to
>>>>>> consider the control mechanism for the alula to be *part* of the
>>>>>> alula?
>>>>> Yes. But part of something isn't that same as that thing. So your
>>>>> question had to be answered in the negative.
>>>>
>>>> So it *is* part of the alula. So is the part you mentioned. They are
>>>> both parts, not the whole. You made a false distinction.
>>>
>>> Not that I can see.
>>>
>>
>>
>

[jillery]

On Sun, 15 Jan 2012 17:22:27 -0800, John Harshman
<jhar...@pacbell.net> wrote:

>Friar Broccoli wrote:

[...]

>> So does digit IV become III? Or do we count 1, 2, 4 or something like
>> that?
>
>According to the frame shift hypothesis, I, II, III become II, III, IV.
>The standard amniote phalangeal formula is 2-3-4-5-4. The standard
>theropod formula is 2-3-4. You figure it.

Everything I know about the frame-shift hypothesis I read in PZ's
article, so I'm not pretending any expertise here. But according to
PZ's article, you have it exactly backwards. The bird embryo resorbs
CI, so it can't become anything. Instead CII, CIII, CIV becomes DI,
DII, DIII.

[jillery]

On Sun, 15 Jan 2012 17:29:24 -0800, John Harshman
<jhar...@pacbell.net> wrote:

[...]

>> But the actual digit identities of these condensations, what makes CI
>> a thumb etc, is established in a much later step. It's that step
>> which presumably frame-shifted, so that CII becomes DI, CIII becomes
>> DII, and CIV become DIII.
>
>Exactly. So if we're talking about digits rather than condensations,
>birds have DI, DII, and DIII.

ISTM a moot distinction wrt birds, considering bird fingers are
(mostly) fused anyway. If I had a vote, which I don't, it would be
to identify fingers based on from whence they came, as does Myers, and
not on their secondarily derived function, as does Nash.

>> Like I said, it makes sense to me.
>>
>>>>>> More important question, I don't understand the distinction you're
>>>>>> trying to make. Are you suggesting birds' alula are passive
>>>>>> mechanisms?
>>>>> No. What gave that impression?
>>>> It is the only way I knew how make sense of what you wrote.
>>> Then you need to find another way. I don't understand your interpretation.
>>
>> You asked a question. I answered it honestly. Only after I answered
>> did you say I was wrong, but I still don't understand the distinction
>> you're trying to make below.
>
>You're wrong about that too.

WTF??

>I said you were wrong,

about what you were talking about being the alula, yes.

> and then asked what
>made you think otherwise.

And then I answered. And then you wrote "You need to find another way"
ie I am wrong (again). So I'm right.

>The distinction is simple. The digit isn't the
>allula. It's the skeletal portion of the allula.

Yes, the digit part of the alula, the part about which I originally
asked, the part which you described the hoatzin using to climb around.
Your distinction might be simplie, but your negativity smears it
beyond recognition.

>>>>>> IIUC birds have direct control of when and how much to
>>>>>> extend it, typically just before landing. Is it not reasonable to
>>>>>> consider the control mechanism for the alula to be *part* of the
>>>>>> alula?
>>>>> Yes. But part of something isn't that same as that thing. So your
>>>>> question had to be answered in the negative.
>>>> So it *is* part of the alula. So is the part you mentioned. They are
>>>> both parts, not the whole. You made a false distinction.
>>> Not that I can see.
>>
>> Let's try this. I stipulate for argument's sake birds' wings include
>> a thumb. You wrote above the thumb is part of an alula. This implies
>> there are *other* parts of an alula. That part of the wing you
>> identified as attached to the thumb is also *part* of an alula A
>> complete alula is the entire collection of all its parts. If you
>> remove any part, you no longer have a complete alula. I identified
>> *part* of an alula. You identified *part* of an alula. The part you
>> identified is no more a complete alula than is my part. Parts is
>> parts. Our statements are equivalent. You made a false distinction.
>
>Ah, I see what you mean. OK, what I said was wrong too. The allula is
>the entire package. Now are we agreed on that point?

Of course, but that isn't what I would have understood from your
original "no". ISTM you contradict yourself but won't admit it.

[pnyikos]

On Jan 13, 5:12 pm, Arkalen <arka...@inbox.com> wrote:

> (2012/01/14 6:38), pnyikos wrote:
> > On Jan 13, 3:12 pm, John Harshman<jharsh...@pacbell.net>  wrote:

> >> Arkalen wrote:
> >>> (2012/01/14 4:17), Metspitzer wrote:
> >>>> It wasn't a trick question it was just a typo.
>
> >>>> Also, were there any avian dinosaurs that walked on four legs?
>
> >>> Don't all avian dinosaurs have wings ? It would depend on which
> >>> dinosaurs are "avian". If they include dinosaurs with wings that still
> >>> have claws and all that stuff like Archaeopteryx, then theoretically I
> >>> suppose a secondarily flightless dinosaur in that group could have
> >>> walked on four legs. I don't think we know of any such dinosaur.
>

> >> It's vaguely conceivable that some therizinosaurs were quadrupedal.
>
> > Here's another question for you: were pterosaurs bipedal or
> > quadrupedal?
>

> > And another: if bipedal, which two feet did they walk on?
>

> > In re the former question, John Ostrom's answer is "quadrupedal" but
> > back in the 1990's one of our resident paleontologists in s.b.p.
> > claimed they were bipedal.
>

> > Google seems to have dropped our exchange on that.  As well as I
> > recall, I told him:
>
> > "For what it's worth, John Ostrom disagrees with you" and then I
> > quoted something from an article by Ostrom, giving a precise
> > reference.
>

> > "I am aware of the mild disagreement between John and myself..." was
> > about how he began.
>
> > In re the latter question: the South Carolina Museum, here in
> > Columbia, once hosted a traveling exhibit on the land vertebrates of
> > the Mesozoic, and one life-size exhibit was a model of Pteranodon
> > walking on its front feet, with the hind feet suspended in air.
>

> > A famous writer once did a science fiction story about a species in

> > the Galactic Federation (not sure that was what he called it) which

> > had an intelligent species of the same sort in it.
>
> > IIRC the author was Poul Anderson, and what I saw was a first
> > installment in a science fiction magazine, with a picture showing one
> > of the members of the species sitting at a bar, holding a drink with
> > one of its "hind hands".
>

> You'd only call them "hind hands" as opposed to "hands" if there were
> also "forehands". Sounds to me like that alien species is
> chimpanzee-like more than anything.

In that respect, maybe. But they were able to fly, and that was
worked into the story in a big way.

> But you read the story, maybe they
> specified in it that it was a creature with its back limbs as hands and
> front limbs as feet.

Alas, I last read the story four decades ago, and I can't recall
whether it said anything about the manipulative abilities of the front
feet. I also can't recall what happened to my copy of the first
installment.

> Either way that sounds to me like a very unlikely combination, because
> if you're going to have hands it's presumably to use them, and in that
> case you'll want them to be close to where most of your sensory organs
> are, i.e. the head.

As in chimps? Their hind hands are worthy of the name IMO.

Also, IIRC the digits in the Poul Anderson saga were like in
pterosaurs, or else it was the "little" finger that expanded
enormously, leaving the possibility of thumbs developing on the other
side.

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

>
> --
> Arkalen
> Praise be to magic Woody-Allen zombie superhero telepathic vampire
> quantum hovercraft Tim! Jesus.

Any reason why these particular words are jumbled together?

Peter Nyikos

[pnyikos]

On Jan 13, 9:28 pm, John Harshman <jharsh...@pacbell.net> wrote:
> Will in New Haven wrote:

> > On Jan 13, 7:05 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >> pnyikos wrote:
> >>> On Jan 13, 3:12 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >>>> Arkalen wrote:
> >>>>> (2012/01/14 4:17), Metspitzer wrote:
> >>>>>> It wasn't a trick question it was just a typo.
> >>>>>> Also, were there any avian dinosaurs that walked on four legs?
> >>>>> Don't all avian dinosaurs have wings ? It would depend on which
> >>>>> dinosaurs are "avian". If they include dinosaurs with wings that still
> >>>>> have claws and all that stuff like Archaeopteryx, then theoretically I
> >>>>> suppose a secondarily flightless dinosaur in that group could have
> >>>>> walked on four legs. I don't think we know of any such dinosaur.
> >>>> It's vaguely conceivable that some therizinosaurs were quadrupedal.
>
> >>> Here's another question for you: were pterosaurs bipedal or
> >>> quadrupedal?
> >> Current consensus is the latter.
>
> >>> And another: if bipedal, which two feet did they walk on?
> >> Are you seriously entertaining the idea of pterosaurs walking on their
> >> hands? If so, you've been reading too much Poul Anderson.

Wrong. I wouldn't have taken Anderson seriously were it not for the
traveling exhibit I told you about.

__________ begin repost_______

In re the latter question: the South Carolina Museum, here in
Columbia, once hosted a traveling exhibit on the land vertebrates of
the Mesozoic, and one life-size exhibit was a model of Pteranodon
walking on its front feet, with the hind feet suspended in air.

================end of repost

By the way, the official name of the museum is the South Carolina
State Museum. It's well worth a look if one happens to have a free
day or two in Columbia, although I rate the Riverbanks Zoo even
higher.

Will in New Haven wrote on "too much Poul Anderson":

> > Can't be done. I've read everything he wrote, including non-fiction.
> > Some of it wasn't as good as the rest but none of it was too much. And
> > there won't be anymore.

A researcher in measure theory who spent several days as our house
guest is a science buff, and read "The Avatar" from cover to cover
while with us. His verdict was that success had spoiled Anderson to
where he padded his story to about twice the length it deserved.

> Actually, I've read a couple of quite bad books by Anderson. One was
> apparently a very early effort, and the other was an attempt at
> "mainstream" fiction.
>
> But I take your point.

Good. My two favorites of Poul Anderson are the short story
"Epilogue" and the nonfiction "Is There Life on Other Worlds?" I
haven't read "Tau Zero" yet -- some say is his best novel. "Brain
Wave" and "We Claim These Stars" are both reasonably good novels, but
they can't compare with "Epilogue" for sheer drama and
characterization.

"Epilogue" is right up there with Roger Zelazny's "For a Breath I
Tarry" and it's a shame there are so few anthologies nowadays that
include either one of these.

Peter Nyikos

[Arkalen]

Others have responded to you recognizing the story you were talking
about and didn't disagree with your characterization at all so I think
you must have been correct, and my interpretation of what the terms
meant was wrong.

>
>> Either way that sounds to me like a very unlikely combination, because
>> if you're going to have hands it's presumably to use them, and in that
>> case you'll want them to be close to where most of your sensory organs
>> are, i.e. the head.
>
> As in chimps? Their hind hands are worthy of the name IMO.

My objection is specifically to the concept that organisms would evolve
that used their hind limbs for manipulating things and their front limbs
for walking. Chimps use both their front hands and their hind hands.
Parrots use their legs for manipulation, but they also use them for
walking and everything else; in practice those are the only limbs they
have because their wings are too specialized to be useful for anything
other than flying, or activities very close to flying (like penguins in
water, as Ernest Major pointed out)

Note that this was originally about the question of whether Pteranodons
walked on their front or back limbs. If we're looking at alien species,
I have since thought of ways organisms could evolve to use their hind
limbs preferentially for manipulating things (see spiders), so I now
find the concept less implausible than I did at first. But spiders have
a very specific reason why they might evolve to use their back legs for
manipulating things while using front legs for locomotion. Pteranodons
(or any tetrapod for that matter) don't have such a reason that I can see.

[Friar Broccoli]

On 2012-01-15 23:26, jillery wrote:
> On Sun, 15 Jan 2012 17:22:27 -0800, John Harshman
> <jhar...@pacbell.net> wrote:
>
>> Friar Broccoli wrote:
>
> [...]
>
>>> So does digit IV become III? Or do we count 1, 2, 4 or something like
>>> that?
>>

.

>> According to the frame shift hypothesis, I, II, III become II, III, IV.
>> The standard amniote phalangeal formula is 2-3-4-5-4. The standard
>> theropod formula is 2-3-4. You figure it.
>
>
> Everything I know about the frame-shift hypothesis I read in PZ's
> article, so I'm not pretending any expertise here. But according to
> PZ's article, you have it exactly backwards.

I don't see this. It appears to me that "become" is ambiguous here.
Above Harshman is using "become" as 'the existing (anatomically
designated) Digits become the since discovered (developmentally
designated) Condensations' so his timeline is the order of discovery,
while below you are using "become" in an order of evolutionary event
timeline sense, so you are both saying the same thing.

> The bird embryo resorbs
> CI, so it can't become anything. Instead CII, CIII, CIV becomes DI,
> DII, DIII.

On the wider question note that Harshman's original statement was:
"There is no reasonable sense in which it's digit II." a clear
reference to the anatomical assignment D.

>
>
>>>>>>> More important question, I don't understand the distinction you're
>>>>>>> trying to make. Are you suggesting birds' alula are passive
>>>>>>> mechanisms?
>>>>>> No. What gave that impression?
>>>>>
>>>>> It is the only way I knew how make sense of what you wrote.
>>>>
>>>> Then you need to find another way. I don't understand your
>>>> interpretation.
>>>>
>>>>>>> IIUC birds have direct control of when and how much to
>>>>>>> extend it, typically just before landing. Is it not reasonable to
>>>>>>> consider the control mechanism for the alula to be *part* of the
>>>>>>> alula?
>>>>>> Yes. But part of something isn't that same as that thing. So your
>>>>>> question had to be answered in the negative.
>>>>>
>>>>> So it *is* part of the alula. So is the part you mentioned. They are
>>>>> both parts, not the whole. You made a false distinction.
>>>>
>>>> Not that I can see.
>>>>
>>>
>>>
>

[John Harshman]

jillery wrote:
> On Sun, 15 Jan 2012 17:22:27 -0800, John Harshman
> <jhar...@pacbell.net> wrote:
>
>> Friar Broccoli wrote:
>
> [...]
>
>>> So does digit IV become III? Or do we count 1, 2, 4 or something like
>>> that?
>> According to the frame shift hypothesis, I, II, III become II, III, IV.
>> The standard amniote phalangeal formula is 2-3-4-5-4. The standard
>> theropod formula is 2-3-4. You figure it.
>
>
> Everything I know about the frame-shift hypothesis I read in PZ's
> article, so I'm not pretending any expertise here. But according to
> PZ's article, you have it exactly backwards. The bird embryo resorbs
> CI, so it can't become anything. Instead CII, CIII, CIV becomes DI,
> DII, DIII.

That is indeed what I meant to say. Sorry.

You can read the frameshift hypothesis in its original in Wagner, G. P.,
and J. A. Gauthier. 1999. 1, 2, 3 = 2, 3, 4: A solution to the problem
of the homology of the digits in the avian hand. Proceedings of the
National Academy of Sciences 96:5111-5116.

Which you can find at
http://www.pnas.org/content/96/9/5111.full?sid=192e8df0-659d-48c8-b413-a08c27799750

[John Harshman]

Friar Broccoli wrote:
> On 2012-01-15 23:26, jillery wrote:
>> On Sun, 15 Jan 2012 17:22:27 -0800, John Harshman
>> <jhar...@pacbell.net> wrote:
>>
>>> Friar Broccoli wrote:
>>
>> [...]
>>
>>>> So does digit IV become III? Or do we count 1, 2, 4 or something like
>>>> that?
>>>
>
> .
>
>>> According to the frame shift hypothesis, I, II, III become II, III, IV.
>>> The standard amniote phalangeal formula is 2-3-4-5-4. The standard
>>> theropod formula is 2-3-4. You figure it.
>>
>>
>> Everything I know about the frame-shift hypothesis I read in PZ's
>> article, so I'm not pretending any expertise here. But according to
>> PZ's article, you have it exactly backwards.
>
> I don't see this. It appears to me that "become" is ambiguous here.
> Above Harshman is using "become" as 'the existing (anatomically
> designated) Digits become the since discovered (developmentally
> designated) Condensations' so his timeline is the order of discovery,
> while below you are using "become" in an order of evolutionary event
> timeline sense, so you are both saying the same thing.

Nice save, but indeed I just said it backwards from what I intended.

[Greg G.]

On Jan 13, 3:11 pm, John Harshman <jharsh...@pacbell.net> wrote:
> Richard Norman wrote:
> > On Fri, 13 Jan 2012 14:17:32 -0500, Metspitzer <kilow...@charter.net>

> > wrote:
>
> >> It wasn't a trick question it was just a typo.
>
> >> Also, were there any avian dinosaurs that walked on four legs?
>

> > What do you mean by "avian dinosaur"?
>
> "Bird"?

Penguins are the best quadrupedal avian dinosaurs as they slide
through snow on their bellies. pushing with their feet and steering
with their wings.

[jillery]

On Mon, 16 Jan 2012 11:06:43 -0500, Friar Broccoli <eli...@gmail.com>
wrote:

>On 2012-01-15 23:26, jillery wrote:
>> On Sun, 15 Jan 2012 17:22:27 -0800, John Harshman
>> <jhar...@pacbell.net> wrote:
>>
>>> Friar Broccoli wrote:
>>
>> [...]
>>
>>>> So does digit IV become III? Or do we count 1, 2, 4 or something like
>>>> that?
>>>

>>> According to the frame shift hypothesis, I, II, III become II, III, IV.
>>> The standard amniote phalangeal formula is 2-3-4-5-4. The standard
>>> theropod formula is 2-3-4. You figure it.
>>
>>
>> Everything I know about the frame-shift hypothesis I read in PZ's
>> article, so I'm not pretending any expertise here. But according to
>> PZ's article, you have it exactly backwards.
>
>I don't see this. It appears to me that "become" is ambiguous here.
>Above Harshman is using "become" as 'the existing (anatomically
>designated) Digits become the since discovered (developmentally
>designated) Condensations' so his timeline is the order of discovery,
>while below you are using "become" in an order of evolutionary event
>timeline sense, so you are both saying the same thing.

Hopefully you read Harshman's demurral, and I will leave it at that.

>> The bird embryo resorbs
>> CI, so it can't become anything. Instead CII, CIII, CIV becomes DI,
>> DII, DIII.
>
>On the wider question note that Harshman's original statement was:
>"There is no reasonable sense in which it's digit II." a clear
>reference to the anatomical assignment D.

At first blush, it looks like just an arcane argument over a pedantic
point about how to label digits. I mean, so what? After all, a rose
by any other name, and presumably so too a digit, would smell as
sweet. Is this really something worth worrying about?

But the real issue behind the naming is profoundly important. As
Wagner and Gauthier explained, both embryology and morphology have
strong evidence for their conclusions, and appeared opposed to each
other. This conflict can't be resolved by rejecting one kind of data
or by assuming birds are not theropod dinosaurs. The frame-shift
hypothesis provides a plausible solution to the paradox, one that can
be tested against additional evidence and still remain consistent with
the Theory of Evolution and Common Descent.

[jillery]

On Mon, 16 Jan 2012 08:11:14 -0800, John Harshman

<jhar...@pacbell.net> wrote:

>jillery wrote:
>> On Sun, 15 Jan 2012 17:22:27 -0800, John Harshman
>> <jhar...@pacbell.net> wrote:
>>
>>> Friar Broccoli wrote:
>>
>> [...]
>>
>>>> So does digit IV become III? Or do we count 1, 2, 4 or something like
>>>> that?
>>> According to the frame shift hypothesis, I, II, III become II, III, IV.
>>> The standard amniote phalangeal formula is 2-3-4-5-4. The standard
>>> theropod formula is 2-3-4. You figure it.
>>
>>
>> Everything I know about the frame-shift hypothesis I read in PZ's
>> article, so I'm not pretending any expertise here. But according to
>> PZ's article, you have it exactly backwards. The bird embryo resorbs
>> CI, so it can't become anything. Instead CII, CIII, CIV becomes DI,
>> DII, DIII.
>
>That is indeed what I meant to say. Sorry.

NP

>You can read the frameshift hypothesis in its original in Wagner, G. P.,
>and J. A. Gauthier. 1999. 1, 2, 3 = 2, 3, 4: A solution to the problem
>of the homology of the digits in the avian hand. Proceedings of the
>National Academy of Sciences 96:5111-5116.
>
>Which you can find at
>http://www.pnas.org/content/96/9/5111.full?sid=192e8df0-659d-48c8-b413-a08c27799750

Yes, this is the paper Myers cited in his article I cited. One of the
things Wagner and Gauthier specifically write is there are
segmentation genes, which control the development of the digit
condensations, and homeotic genes, which determine their actual
identity. These separate sets of genes are active at separate times
in embryological development.

Presumably a separate but similar set of segmentation and homeotic
genes control the development of toes in a similar way. Their article
implies, but does not say, that there is no similar conflict wrt bird
toes, and so no frame-shift is required for them.

When their article was first published in 1998, a detailed genome map
of birds was not available. But since then, a number of bird species
have had their genomes mapped. Would it be possible in principle to
look at bird genomes, identify the segmentation and homeotic genes for
fingers and for toes, and see if there are any differences which could
reasonably be considered evidence for this hypothetical frame-shift?
Has this been done already?

[John Harshman]

Yes, assuming that 3 is considered to be a number. So far there are
approximately complete releases of chicken, turkey, and zebra finch.
More are in process. But genomes don't really help all that much. What
you really need is expression data. Then you can target small parts of
the genome that are candidates for the crucial changes; complete genomes
just have too much going on.

> Would it be possible in principle to
> look at bird genomes, identify the segmentation and homeotic genes for
> fingers and for toes, and see if there are any differences which could
> reasonably be considered evidence for this hypothetical frame-shift?

In principle, perhaps. It wouldn't be the genes, per se, but the
regulatory sequences that would likely have caused the change. The first
thing to do would be to check not the genomes but the patterns of gene
expression. Only after identifying the relevant differences would we
have an idea of where to look in the genomes. And it's currently hard to
predict from looking at the sequence itself what a regulatory sequence
does, so the genetic basis of expression patterns may be a while in coming.

> Has this been done already?

No. But there are a number of papers on gene expression that provide
clues. The expression pattern, so far as it has been identified, is
consistent with I-II-III. I don't think any of the expression data so
far would be able to distinguish a frame shift from a plain vanilla
I-II-III hypothesis. But at least the simple II-III-IV is out.

Here are a couple I happen to have handy:

Dahn, R. D., and J. F. Fallon. 2000. Interdigital regulation of digit
identity and homeotic transformation by modulated BMP signaling. Science
289:438-441.
Galis, F. 2001. Digit identity and digit number: Indirect support for
the descent of birds from theropod dinosaurs. Trends in Ecology and
Evolution 16:16.

I haven't been paying attention for a while, and there's probably a lot
more that's more recent.

[jillery]

On Tue, 17 Jan 2012 07:45:44 -0800, John Harshman

What a bizarre thing to write. Why would anyone assume 3 to be *not*
a number? It's 3 more than were available when the article was first
published. Would it help to mention the black-throated hummingbird's
genome is now mapped, making the number 4? Do you have some esthetic
objection to 3? Perhaps you have a distaste for prime numbers? Or do
you just want to imply disaffection about something but aren't willing
to state what it is explicitly?

Thank you for these. Obviously, I'm not familiar enough with the
mechanics of genetic frame-shifts to make even reasonable speculations
about them.

[John Harshman]

What you would need to find would be the mutations that specifically
caused the expression pattern to move down one condensation. This is
made difficult by the lack of study organisms close to the crucial
event. As it is, one would have to compare chickens with alligators. And
whatever it is must be complicated, because early theropods had 5 digits
with digits IV and V reduced to rudiments. This alone is a very strange
and unexpected developmental pattern -- digit I should, in all sensible
tetrapods, be reduced before digit IV. Why there should at that point be
a frame shift, rather than just a continuing decline of the already
oddly small digits, is even harder to understand.

[jillery]

On Wed, 18 Jan 2012 08:50:38 -0800, John Harshman

No response to this?

IIUC the frame-shift didn't happen because it needed to happen. It
happened as a matter of course, as have other documented frame-shifts,
and this particular one provided an advantage for those particular
animals in that particular environment.

[John Stockwell]

On Jan 13, 12:17 pm, Metspitzer <kilow...@charter.net> wrote:
> It wasn't a trick question it was just a typo.
>
> Also, were there any avian dinosaurs that walked on four legs?

Because there aren't any predecessors that walked on 6 legs.

[John Harshman]

That's bleedin' obvious, but "selection happens" isn't an explanation.

The point is that the really odd thing happened before any frame shift.
All a frame shift explains is that there is a condensation in chicken
embryos craniad to the one that eventually becomes digit I. The weird
situation that digit I is retained while digit IV is lost, or, to put it
another way, the shift of developmental axis from digit IV to digit II,
apparently happened before any frame shift.

[John Harshman]

Let's not forget that pterosaurs apparently walked on 4 legs, so the
idea of a quadrupedal bird isn't completely nonsensical.

[jillery]

On Wed, 18 Jan 2012 14:44:23 -0800, John Harshman

OK then, important enough to complain about, but not important enough
to back up.

I wasn't giving an explanation. ISTM you were making a teleological
conclusion, and I commented on that.

[pnyikos]

> >>>>>>>http://www.pnas.org/content/96/9/5111.full?sid=192e8df0-659d-48c8-b41...

> >>>>>> Yes, this is the paper Myers cited in his article I cited.  One of the
> >>>>>> things Wagner and Gauthier specifically write is there are
> >>>>>> segmentation genes, which control the development of the digit
> >>>>>> condensations, and homeotic genes, which determine their actual
> >>>>>> identity.  These separate sets of genes are active at separate times
> >>>>>> in embryological development.
>
> >>>>>> Presumably a separate but similar set of segmentation and homeotic
> >>>>>> genes control the development of toes in a similar way.  Their article
> >>>>>> implies, but does not say, that there is no similar conflict wrt bird
> >>>>>> toes, and so no frame-shift is required for them.
>
> >>>>>> When their article was first published in 1998, a detailed genome map
> >>>>>> of birds was not available.  But since then, a number of bird species
> >>>>>> have had their genomes mapped.
> >>>>> Yes, assuming that 3 is considered to be a number.
>
> >>>> What a bizarre thing to write.  Why would anyone assume 3 to be *not*
> >>>> a number?

ISTM Harshman was referring to your comment a few lines earlier,

"a number of bird species
have had their genomes mapped."

Perhaps he was belittling the small size of the sample. And if one
wants a really good phylogenetic tree of birds, one would want a
goodly number of genomes to be mapped.

Of course, one can get good phylogenetic trees with just some parts of
genomes, but I set high standards on "really good." YMMV.

BTW it looks like you caught on to Harshman's intended meaning in your
very next sentence:

> >>>> It's 3 more than were available when the article was first
> >>>> published.  Would it help to mention the black-throated hummingbird's
> >>>> genome is now mapped, making the number 4?

...but then you seemed to drift away from it again:

> >>>>  Do you have some esthetic
> >>>> objection to 3?  Perhaps you have a distaste for prime numbers?  Or do
> >>>> you just want to imply disaffection about something but aren't willing
> >>>> to state what it is explicitly?
>
> >> No response to this?
>
> OK then, important enough to complain about, but not important enough
> to back up.

Are you reading what he wrote as some sort of complaint?

By the way, believe it or not, I like PZ Myers's (arbitrary, in the
last analysis) numbering better than the one Harshman seemed to be
leaning towards. It's nice to have the numbering reflect the
homology.


[...]

>>>>digit I should, in all sensible
>>>> tetrapods, be reduced before digit IV. Why there should at that point be
>>>> a frame shift, rather than just a continuing decline of the already
>>>> oddly small digits, is even harder to understand.

> >> IIUC the frame-shift didn't happen because it needed to happen.

IIU Harshman C, he was using "should be" in a different sense than you
seem to think he was using it.

> >>It happened as a matter of course, as have other documented frame-shifts,
> >> and this particular one provided an advantage for those particular
> >> animals in that particular environment.

Ah, yes, the "Darwin of the Gaps" argument for why it happened. Why
might genetic drift not be an acceptable alternative explanation? Do
you have specialized knowledge of what that particular environment was
like, and why the frame shift provided an advantage?

> >That's bleedin' obvious, but "selection happens" isn't an explanation.
>
> I wasn't giving an explanation.  ISTM you were making a teleological
> conclusion, and I commented on that.

It doesn't seem that way to me. ISTM he was just using an idiom for
"It looks weird--why did it happen, anyway?" See below.

> >The point is that the really odd thing happened before any frame shift.
> >All a frame shift explains is that there is a condensation in chicken
> >embryos craniad to the one that eventually becomes digit I. The weird
> >situation that digit I is retained while digit IV is lost, or, to put it
> >another way, the shift of developmental axis from digit IV to digit II,
> >apparently happened before any frame shift.

Peter Nyikos

[John Harshman]

Missed this the first time around. As far as I can tell, your claim
about the black-chinned hummingbird is not true. I speculate that you
gained that impression from frequent web statements that it has the
smallest known genome of any bird. But you don't need to map (or
sequence, which is what you really mean) the genome to find that out. As
far as the UCSC genome browser knows, there still only 3 bird genome
projects that have published drafts: chicken, turkey, and zebra finch.
Is this enough to tell us anything about the genes responsible for any
frame shift? Very doubtful. If anything, you need an alligator (and the
alligator genome project is in progress) and several birds, most likely
including a paleognath (several projects in progress), a galloanserine
(annoying, two with current drafts), and a neoavian or two (one with
drafts, several in progress).

[jillery]

On Fri, 27 Jan 2012 12:30:51 -0800, John Harshman

And you still missed it. Perhaps you should re-sight your 'scope.

>As far as I can tell, your claim
>about the black-chinned hummingbird is not true. I speculate that you
>gained that impression from frequent web statements that it has the
>smallest known genome of any bird. But you don't need to map (or
>sequence, which is what you really mean) the genome to find that out. As
>far as the UCSC genome browser knows, there still only 3 bird genome
>projects that have published drafts: chicken, turkey, and zebra finch.
>Is this enough to tell us anything about the genes responsible for any
>frame shift? Very doubtful. If anything, you need an alligator (and the
>alligator genome project is in progress) and several birds, most likely
>including a paleognath (several projects in progress), a galloanserine
>(annoying, two with current drafts), and a neoavian or two (one with
>drafts, several in progress).

Pedantic obfuscation noted.

[John Harshman]

Ah, well. I tried. But I'm only trying once.

[jillery]

On Fri, 27 Jan 2012 18:54:32 -0800, John Harshman

Not even close.

>But I'm only trying once.

I tried 3 times, and you still "missed" it.

[John Harshman]

Do you sometimes post under the name "JTEM"?

[jillery]

On Sat, 28 Jan 2012 06:54:15 -0800, John Harshman
<jhar...@pacbell.net> wrote:

>Do you sometimes post under the name "JTEM"?

That's your pseudonym

[jillery]

On Sat, 28 Jan 2012 12:43:29 -0500, jillery <69jp...@gmail.com>
wrote:

You're the one repeatedly resorting to ad hominems.

[pnyikos]

> >>>>>http://www.pnas.org/content/96/9/5111.full?sid=192e8df0-659d-48c8-b41...

>
> >>>> Yes, this is the paper Myers cited in his article I cited.  One of the
> >>>> things Wagner and Gauthier specifically write is there are
> >>>> segmentation genes, which control the development of the digit
> >>>> condensations, and homeotic genes, which determine their actual
> >>>> identity.  These separate sets of genes are active at separate times
> >>>> in embryological development.
>
> >>>> Presumably a separate but similar set of segmentation and homeotic
> >>>> genes control the development of toes in a similar way.  Their article
> >>>> implies, but does not say, that there is no similar conflict wrt bird
> >>>> toes, and so no frame-shift is required for them.
>
> >>>> When their article was first published in 1998, a detailed genome map
> >>>> of birds was not available.  But since then, a number of bird species
> >>>> have had their genomes mapped.
> >>> Yes, assuming that 3 is considered to be a number.
>
> >> What a bizarre thing to write.  Why would anyone assume 3 to be *not*
> >> a number?  It's 3 more than were available when the article was first
> >> published.

Now we come to another on-topic statement by "jillery":

> >>  Would it help to mention the black-throated hummingbird's
> >> genome is now mapped, making the number 4?

Harshman addressed this claim below, but "jillery" evidently preferred
to wallow in an off-topic brouhaha, starting with the her/his parting
shot below, and continuing for two rounds of back and forth, followed
by yet another post with a gratuitous insult.

> > > Do you have some esthetic
> >> objection to 3?  Perhaps you have a distaste for prime numbers?  Or do
> >> you just want to imply disaffection about something but aren't willing
> >> to state what it is explicitly?
>
> >Missed this the first time around.
>
> And you still missed it.  Perhaps you should re-sight your 'scope.
>
> >As far as I can tell, your claim
> >about the black-chinned hummingbird is not true. I speculate that you
> >gained that impression from frequent web statements that it has the
> >smallest known genome of any bird. But you don't need to map (or
> >sequence, which is what you really mean) the genome to find that out. As
> >far as the UCSC genome browser knows, there still only 3 bird genome
> >projects that have published drafts: chicken, turkey, and zebra finch.
> >Is this enough to tell us anything about the genes responsible for any
> >frame shift? Very doubtful. If anything, you need an alligator (and the
> >alligator genome project is in progress) and several birds, most likely
> >including a paleognath (several projects in progress), a galloanserine
> >(annoying, two with current drafts), and a neoavian or two (one with
> >drafts, several in progress).
>
> Pedantic obfuscation noted.

Desire to get back to an off-topic personal brouhaha, with a meaty, on-
topic statement labeled as "pedantic obfuscation," noted.

If "jillery" runs true to form, [s]he will flame me for indulging in a
personal attack and "invite" me to discuss some on-topic issue.

That is, if 'e notices this post at all. It's been three weeks since
'e last posted to this thread.

Peter Nyikos

[John Stockwell]

Clearly the individual was thinking of a Pegasus type situation,
rather than a claw walking batlike thing analogy.