Dinosaur lungs

Cool.

But, where is evolution going now?

http://www.askboz.com/asktationmn.html

With that kind of speed available, it's a miracle the Ark got away from those murderous T-Rexses.

Whoops, it was explained to me in vertebrate anatomy that one thing the air sac definitely do not do is make a bird lighter. The hollow bones do lighten a bird because they replace the function of something heavier. The air sacs do not replace any heavier organs (unless the lungs are smaller because of the arrangement, but I don't think you are arguing that is their primitive function). The air sacs lower a birds' density, but that is not the same thing as its mass.

Thanks -- I love stuff like this. For what it's worth, nobody gets the better of the birds in my back yard either -- they're pretty fierce little creatures.

If you have any knowledge or links for the following questions, could you please post?:

Is this relevant to all dinosaurs, or is there speculation that ancestors of reptiles and ancestors of birds were both dinosaurs and diverged?

Is the high metabolic rate of dinosaurs implicated in their extinction?

Is it possible the dinosaurs just 'miniaturized' into birds (similar to the way pygmy forms of emigrant animals adapt to island habitats)?

I love this stuff. Great post PZ.

Heather, here's some info that may help with your question.

http://www.kurzweilai.net

Modern reptiles fall into three main groups. Turtles and tortoises, crocodiles, and snakes and lizards.

Dinosaurs and crocs fall into the larger grouping called Archosauria. Crocs are not descended from any dinosaur, rather they shared a common ancestor with the animal that gave rise to all dinosaurs (and eventually birds).

The snakes and lizards belong to another group of reptiles entirely, called the Lepidosauria. Their last common ancestor with crocs lived long before this, probably sometime in the Permian.

Both these groups (along with several extinct forms) are a subdivision of the reptiles called diapsids (they have two openings on the side of the skull behind the name). Turtles and tortoises do not have this opening and are placed in a more primitive group called the anapsids (they don't have any openings in the skull behind the eye).

It turns out that the tortoises probably aren't anapsids after all, but diapsids that have lost the skull openings. Where exactly they fit in that case is uncertain, but they aren't archosaurs.

Hi meridan,
I'd also LOVE a paleontologist to expand on any or all of these questions. What I've read in my small amount of reading is...

Is this relevant to all dinosaurs, or is there speculation that ancestors of reptiles and ancestors of birds were both dinosaurs and diverged?
-Seems to be for the theropods at least, and that birds are indeed true dinosaurs, so they did not entirely go extinct.

Is the high metabolic rate of dinosaurs implicated in their extinction?
-My question also. In the extinction theories, nobody I've seen addresses how at least some birds went through the event, but other dino's, large and small did not. I just watch a show on the KT impact, they theorized "large animals couldn't tunnel underground for protection, like mammals". But neither could birds, and amphibians, (great indicator species) also seems to fair well. To me, there seems to be a missing component. Can't wait to hear of the latest/next findings on this. Another interesting part of this is evidently during the Permian extinction, oxygen levels fell dramatically, so an animal with advanced lungs, like early dinosaurs, would be able to exploit the open ecological niches, which may have lead to the dinosaur age.

Is it possible the dinosaurs just 'miniaturized' into birds (similar to the way pygmy forms of emigrant animals adapt to island habitats)?
-Birds as we know them, and a whole line of other birds, commonly called "opposite birds" were evidently common. I've read that ducks, geese, and cranes lived during the Cretaeous period. Scientists classify them closest to theropods, so, (to layman me) they are indeed shrunken T-Rexes, or related to. New finds in China have found theropods with feathers that were clearly not birds at all. So feathers, the defining trait of birds, is indeed a dinosaur one as well. Many scientists have already reclassified birds as dinosaurs. Makes watching the antics at the bird feeder a whole new experience!

Fasinating, utterly fasinating! I never knew this. Clearly it was designed.... (just kidding folks)

But it was designed, and selected....by nature!

"Next time you're cutting up a fresh bird?"

...

...

PZ: Aside from bird lungs, I'm curious about this:

If humans hyperventilate, we pass out. But dogs do it regularly as a device for cooling. Any ideas how dogs can pant rapidly without over-oxygenating their blood?

I think this too is a fascinating evolutionary question. And come to think of it, I've observed birds with their mouths open on really hot days. Are they also panting? Does the same protective mechanism apply?

...

...

"PZ: Aside from bird lungs, I'm curious about this:
If humans hyperventilate, we pass out. But dogs do it regularly as a device for cooling. Any ideas how dogs can pant rapidly without over-oxygenating their blood?
I think this too is a fascinating evolutionary question. And come to think of it, I've observed birds with their mouths open on really hot days. Are they also panting? Does the same protective mechanism apply?"

A dog's heart rate is not the same as ours, and neither are numerous other physiological aspects of a dog as compared to a human...

In short, when we "hyperventilate" our breathing is not in-line with our heart rate and blood flow and diffusion rate ect...
But a Dog, breathing fast, is still in-line with its own heart rates, blood flow ect....

Is it possible the dinosaurs just 'miniaturized' into birds (similar to the way pygmy forms of emigrant animals adapt to island habitats)?

Actually that's an interesting question from another perspective - is it possible that birds had an advantage in their evolution into a small body size while maintaining (or developing) homeothermy by already being in possession of a two-stroke ventilatory system? It's more and more difficult to maintain a constant high body temperature as you get smaller, and it requires an ever-increasing intrinsic metabolic rate as you shrink - maybe the structure of the respiratory system was what allowed theropods to become small, and, at the same time, homeothermic (or retain homeothermy from larger homeothermic ancestors), since they could readily supply their tissues with fresh oxygen from a system already in place. An alternate route to that followed by the mammals, and one requiring less overall morpholigical restructuring.

Arrrrgggghhhh. I meant morphological - how embarrassing. And I see that I also forgot to say that the idea that birds got their start as theropod dinosaurs' evolutionary equivalent of small rodents, exploiting the advantages of simply being small homeotherms, rather than evolving to take advantage of the "aerial vertebrate" lifestyle, is a neat one. An argument for the "ground-up" avian evolution model.

So Gary Larson was right: if the dinosaurs were inhaling like that, they were getting lung cancer even faster!

Damn the copyright laws that make that cartoon impossible to find on teh internets.

Once through ventilation without re-circulation is considered very important in making buildings more energy efficient - because you can maintain air quality with fewer air changes if you don't recirculate. But it is not always easy to implement; you get uneven circulation, dead spots and all sorts of problems. I wonder if bird respiratory systems have something to teach us about how to circulate air within our buildings?

"Arrrrgggghhhh. I meant morphological - how embarrassing. And I see that I also forgot to say that the idea that birds got their start as theropod dinosaurs' evolutionary equivalent of small rodents, exploiting the advantages of simply being small homeotherms, rather than evolving to take advantage of the "aerial vertebrate" lifestyle, is a neat one. An argument for the "ground-up" avian evolution model."

How the hell do you figure that is an argument for ground-up?

Lago-
In answer to your query, birds (like their closest living relatives, the crocodilians) don't pant when they're hot, they gape. Evaporation of moisture from the mucous lining of the mouth generates a cooling effect. In birds, the ventilation rate of the lungs is closely locked in to their locomotion cycle, as it's the squeezing of the trunk during flight muscle contraction that primarily drives the bellows system PZ describes. That means they can't really increase their breathing rate (ie. pant) in response to elevated temperature, and they're doubly screwed because unlike mammals they can't lose heat by sweating either. The reason why sweating hasn't evolved in other lineages isn't clear, but my money would be on the high metabolic cost (it takes an obscene amount of energy to sweat) and the large amount of water used.

"Lago-
In answer to your query, birds (like their closest living relatives, the crocodilians) don't pant when they're hot, they gape. Evaporation of moisture from the mucous lining of the mouth generates a cooling effect. In birds, the ventilation rate of the lungs is closely locked in to their locomotion cycle, ...."

Um, still not seeing how this points towards ground-up here, and not tree-down...

My mistake, I was replying to Mr Fox's earlier post.

Lago-
I think Lars' implication was that the high metabolic rate of birds was an initial adaptation to permit small size in a cursorial (ground-dwelling) niche, and not an adaptation for flight. The traditional trees/cliffs-down model posited a low-energy gliding origin of flight, with the subsequent evolution of elevated metabolism allowing higher-energy flapping flight.

Does anyone know what the lungs were like for non-theropod dinosaurs, like sauropods or ornithischian dinosaurs?

Nice post! I know my human physiology fairly well and it's kind of a shock to remember that we're not necessarily typical of other vertebrates.

A response to Lago's repsonse to Hank Fox: I think I take issue with your explanation.

Humans are perfectly capable of panting too, it's just that we don't really need to do it because we can sweat and dogs don't.

The real difference here is that when we hyperventilate, we take deep breaths, not shallow ones like dogs. If you took lots of shallow, rapid breaths, you would not hyperventilate. In fact, this technique is occasionally used to help patients in ICU settings who are on ventilators to breath when they are difficult to ventilate by standard means.

And the cause of 'hyperventilation', i.e. passing out or getting light-headed, is not actually hyperoxygenation. It's actually a result of blowing off excess CO2. When you do this, you are also blowing off hydrogen ions in the blood (CO2 is in equilibrium with HCO3) and making your blood more alkalotic. Some how (this is the part I don't remember) this causes blood vessle constriction (I think) reducing blood flow to your head, and down you go.

Check out this post.

"Lago-
I think Lars' implication was that the high metabolic rate of birds was an initial adaptation to permit small size in a cursorial (ground-dwelling) niche, and not an adaptation for flight. The traditional trees/cliffs-down model posited a low-energy gliding origin of flight, with the subsequent evolution of elevated metabolism allowing higher-energy flapping flight."

You are putting two things together that are not...

Flight was not linked to the development of the air-sac system, as in it developed before small theropods developed flight. You have made a false correlation. There is nothing about this work that points towards ground-up...

Carpus, I'm interested in checking out the link you provided, but the HTML doesn't work. Would you mind reposting it?

Carpus said: "A response to Lago's response to Hank Fox: I think I take issue with your explanation"

...Actually, I was just oversimplifying things, and I guess one could think I was implying we were passing out due to, "hyperoxygenation", but I wasn't.

Though this is simplistic answer, ..."A dog's heart rate is not the same as ours, and neither are numerous other physiological aspects of a dog as compared to a human..."...It is still accurate...

Lago said: In short, when we "hyperventilate" our breathing is not in-line with our heart rate and blood flow and diffusion rate ect...

Hmmm. I have a naturally slow heart rate, and when I was a kid, I hyperventilated on occasion. Connection? Perhaps with a slower heartbeat it was easier for me to hyperventilate?

Get genetic engineering working really well. I want a pair of these super lungs.

According to the "Flying DNA Hypothesis" it should be sufficient to reduce the size of your genome (but only the noncoding parts) instead of waiting for these super lungs.
PMID: 7566113

>>Flight was not linked to the development of the air-sac system, as in it developed before small theropods developed flight. You have made a false correlation. There is nothing about this work that points towards ground-up...

Lago, I think the implication is that if the air-sac system evolved before flight, then it was probably to aid a faster metabolism and a higher activity level. This removes one of the main supports for a "trees-down" model, which is that an animal with an ectothermic activity pattern can't run fast enough for a flapping take-off, leaving a lower-energy gliding origin of flight as the only likely alternative.
Flight (and a consequent further increase in metabolism and activity levels) may still be the main factor in the elaboration of the air-sac system in birds.

You'd think that air sacs would make it hard/impossible for a bird to dive underwater-- and yet birds do dive and even swim underwater. Is there an extra adaptation that helps here?

Speaking of evolution... online in Nature this week is an incredible paper about a non-coding RNA that is the fastest evolving element in the human genome since our split with chimps. AND it's expressed in the neocortex!

Wow! What a great thread. This is why I keep coming back....that and the sexy cephalopods...

You're a great teacher, PZ.

>>You'd think that air sacs would make it hard/impossible for a bird to dive underwater-- and yet birds do dive and even swim underwater. Is there an extra adaptation that helps here?

Diving birds drastically reduce the level of pneumaticity in the skeleton: this has happened convergently in a number of different lineages, particularly in those which combine diving with flightlessness.

You can pant and not increase your "minute ventilation" - the amount of air moved in and out of your lungs per minute - by taking small enough breaths.

It is the minute ventilation which causes respiratory acidosis or alkalosis.

Fun fact: if you want to impress your friends, most people can hold their breath for up to 2 minutes or more if they hyperventilate beforehand - the human respiratory drive is much more dependent on CO2 levels than it is on O2 levels.

Lycaenops said: "Lago, I think the implication is that if the air-sac system evolved before flight, then it was probably to aid a faster metabolism and a higher activity level. This removes one of the main supports for a "trees-down" model, which is that an animal with an ectothermic activity pattern can't run fast enough for a flapping take-off, leaving a lower-energy gliding origin of flight as the only likely alternative.
Flight (and a consequent further increase in metabolism and activity levels) may still be the main factor in the elaboration of the air-sac system in birds."

Air-sacs evolving with flight is NOT a main support of the hypothesis.

Greg Paul is a major proponent of Tree-Down, and it has always been assumed by him that theropods were feathered, warm-blooded, and with air-sac driven lungs, long before they took to the trees., He even did an amazing job predicting how more basal volant theropods would look years before they were found, and he was dead on the money...

There is nothing in the idea of high metabolism before on takes to the trees that in contradiction with the idea of tree-down. What you have done, is taken a claimed correlation based on people like Ruben and Feduccia (both who assume dinosaurs were cold-blooded creatures) ideas that have no actual basis in reality, and have taken that correlation as real. It isn't.

Think of it this way. No one assumes bats were cold-blooded before they started to evolve flight, correct? Then why the heck should birds have needed to have started out cold-blooded, especially when few think of bats evolving flight from the ground-up?

couple of other points about evaporative and convective body-cooling:
Panting dogs are not in danger of respiratory alkalosis (blowing off too much CO2 and thereby driving up the pH of blood) because they are (mostly) not really breathing--they do not ventilate the lungs but just some of the deadspace in the trachea...inhalation is through the nose and exhalation through the mouth, pushing exhalant air over the moist surfaces of the pharynx (hey...pharyngula) and tongue to increase evaporation. Gas exchange is not much affected. They save energy by panting at the natural resonant frequency of the thorax.
Most birds don't pant (but iirc some do), but many use a technique called "gular fluttering" in which the mouth is held agape and the throat region is rapidly vibrated (bt muscles attaching to the hyoid)...again this does not affect actual gas exchange.
Panting and GF are especially effective at cooling the brain (because of bloodflow patterns in the head & neck region); sweating is better for cooling the entire body surface,but it is expensive energetically (as noted above...the cost comes from active-transport proteins pumping ions across cell membranes), and there are obligate losses of sodium and potassium that can be a problem. Remember the salt pills coaches used to push before Gatorade?
On another subject, probably birds lack scrotums because they can cool their testes convectively by putting them next to a constant-flow airsac. (By the way, the inability to make viable sperm at typical endotherm body temperatures, and thus the need for mammals to hang the family jewels out in the breeze to cool, has to be one of the stupidist bits of Design work out there.)
-Cap'n Comp Physiol

Lago-

Thank you for your interesting reply. Personally, I have no strong views on which of trees-down or ground-up is a better model, but the impression I gain from my colleagues is that the overall functional anatomy of birds and more basal theropods suggests a running origin of flight remains the better explanation. There is still no unequivocal evidence for arboreality in the theropod lineage leading to birds (although this is at least in part due to the taphonomic problems of fossilization in forested environments), and cursoriality is unquestioned in the majority of lineages. The evidence for true endothermic homeothermy in any fossil vertebrate remains equivocal at best: in my own research area of mammalian origins, the fossil record is notably more complete and we still can't agree on the physiology of the animals involved.

In reply to some of your other points:
>even did an amazing job predicting how more basal volant theropods would look years before they were found

There are still no volant theropods known which are more basal than Archaeopteryx. The recent profusion of feathered theropods from China is interesting and provocative, but they can have no direct bearing on the evolution of flight in the lineage leading to birds as they are at least 20 million years after the main event. They may, however, be good evidence for multiple origins of flight within theropods. This may, in turn, suggest that theropods are preadapted for flight due to their possession of feathers (and possibly endothermy).

I don't think Ruben or Feduccia have assumed dinosaurs were 'cold-blooded', they rather consider that the evidence supports it. My considered opinion (for what it's worth) is that a range of thermoregulatory strategies may have been in evidence across the considerable diversity of dinosaurs. In the case of Ruben, he rates soft-tissue evidence as a more accurate indicator of physiology than osteological evidence. His stance is not without merit.

>ideas that have no actual basis in reality
This is not at all useful. Ruben and Feduccia are accomplished scientists, and their opinions deserve to be taken seriously.

Your analogy with bats is also not a useful one. Bats, as mammals, were undoubtedly fully endothermic long before they evolved flight. At present, we cannot say the same thing of birds, although I am of course hopeful that further research will clear up this issue. The gliding origin of bats is reflected in their poor terrestrial locomotory ability, and in the role of the hindlimb in controlling the characteristics of the wing membrane. This may well prove to be the case also in pterosaurs, although the fossil record of their origin is very poor.

Lastly, Greg Paul is something of a dilettante. Unlike papers in scientific journals, books are not peer-reviewed before publication. It's very easy to throw out speculation (and I baulk at your assertion that he "assumed" theropods were feathered etc etc) if you're not the one who has to test it. Bakker had the same problem, and attracted some of the same groupies. The relationship between such factors as flight, feathers, elevated metabolism, homeothermy, growth rates, air-sac ventilation and activity levels remains unclear, and unwarrented assertions by either side do not get us closer to true understanding.

CCP said "couple of other points about evaporative and convective body-cooling:
Panting dogs are not in danger of respiratory alkalosis (blowing off too much CO2 and thereby driving up the pH of blood) because they are (mostly) not really breathing--they do not ventilate the lungs but just some of the deadspace in the trachea...inhalation is through the nose and exhalation through the mouth, pushing exhalant air over the moist surfaces of the pharynx (hey...pharyngula) and tongue to increase evaporation. Gas exchange is not much affected. They save energy by panting at the natural resonant frequency of the thorax."

Yes,...in reality, what I said does not really apply to panting, and applied more to the higher rate of breathing in dogs which would resemble hyperventilating in humans in a relative way. I believe CCP's explanation is the correct one and mine was not a proper answer to the question stated...

Carpus:

"When you do this, you are also blowing off hydrogen ions in the blood (CO2 is in equilibrium with HCO3) and making your blood more alkalotic. Some how (this is the part I don't remember) this causes blood vessle constriction (I think) reducing blood flow to your head, and down you go."

Wikis are getting better:
"If carbon dioxide levels are high, the body assumes that oxygen levels are low, and accordingly the brain's blood vessels dilate, to assure sufficient blood flow and supply of oxygen. Conversely, low carbon dioxide levels (e.g. from hyperventilation) cause the brain's blood vessels to constrict, resulting in reduced blood flow to the brain and lightheadedness."

"The high pH value resulting from hyperventilation also reduces the level of available calcium (hypocalcemia), which affects the nerves and causes the numbness or tingling of the hands. This occurs because alkalinization of the serum proteins (mainly albumin) increases their calcium affinity."
( http://en.wikipedia.org/wiki/Hyperventilation )

When they put the latex into the ducks air sacs, did it hurt the duck? I hope not, I like ducks.

Lycaenops said:
"Lago-
Thank you for your interesting reply. Personally, I have no strong views on which of trees-down or ground-up is a better model, but the impression I gain from my colleagues is that the overall functional anatomy of birds and more basal theropods suggests a running origin of flight remains the better explanation. "

First, the more basal Microraptors I was referring to show all the same signs of being volant as Archaeopteryx does, and I was not referring to animals before Archaeopteryx, but animals more basal to the ones Paul first wrote about at the time he made his prediction and about what these animals would look like closer to a supposed common node between the two...

Next, these same animals, like Microraptors, have numerous signs they were tree climbers. They were very small, had curved digits and sharp claws. They had a much greater degree of mobility in their shoulders, and an increase in the size of their pectorals. They were like-Monkey/cat theropods in their general build.

Also, at least some variations of these animals had large asymmetrical pinnate feathers on their hindlimbs. This does not make for easy ground movement...

One must also remember I am not saying theropods were ground-up, or tree-down in their approach to solving the flight problem. I am saying that being war-blooded is not a barrier against, and to state it as so is "crap science". Saying bats are not relevant to this avoids the fact that we have a precedent in bats for "warm-bloodedness before flight" in at least one group (if it is a singular group) of vertebrates.

On Rubens and Feduccia. If you think either one of those two are simply following the pathway of science (as in the rules of evidence), and where it leads them, and that they have not been disingenuous, or even downright dishonest at times, then I believe you have not taken much time to learn of their tactics over the past few decades.

On Paul not being scientific, this is absurd. Paul writes in an abstract manner, yes, but he makes predictions and compares all ideas side by side (ones he agrees with and ones he does not) to derive his next tentative conclusion that he then tries to make predictions about. Following this Paul has made predictions of avian-like theropods closer to a common node between them and more "extablished basal birds" like Archaeopteryx (even though Archaeopteryx is basically fits fine within these theropod groups as well). It is not speculation to say, "I think you will find dromaeosaurs with pinnate feathers", but a "prediction". And when they are found with pinnate feathers,,,guess what that is?

In short, of course he is doing science...and has been closer to predicting what the fossil record will show than anyone else I can think of when it comes to this subject. Has Feduccia or Ruben's made any predictions of what would be found in the fossil record that back their position that have come true? Care to name me them if so?

RavenT - sorry, I must have blown the link, but it looks like T Larsson (there's an Icelandic name if I ever heard one!) found a nice article with a good explanation. Which is good, because I can't find the site I was referring to!

However, if you're interested, Wikipedia also has an article on high frequency ventilation (let's try this again) here.

Lago-

Thank you very much for your comments. As I said earlier, I have no strong axe to grind on the origins of bird flight, but it would be remiss of me not to attempt to present a reasonably balanced view.

1) The flying capabilities of Microraptor are still a matter for debate. Given that there are no four-winged vertebrates alive today, we have no extant model for comparison which makes it particularly difficult. The best we can do will be to carry out a full biomechanical analysis involving computerised modelling. It takes years to do such things properly.

2) I would contest your statement that Microraptor "shows all the same signs of being volant as Archaeopteryx". It has four wings, for a start, and the rest of its anatomy is distinctly different to reflect their apparently unique mode of flight. (I believe the possibility that one of the Archaeopteryx specimens has feathered hindlimbs has been mooted, but I don't think it's been published yet. I certainly don't remember seeing anything like them on the London holotype). In any event, we shouldn't expect Microraptor to fly like a bird, as it isn't a bird. It likely represents an independent origin of flight within theropods, which (I think) is far more exciting and provocative.

3) There are anatomical correlates of arboreality but they are notoriously difficult to interpret. Sharp claws and grasping feet have almost certainly evolved on occasion for purposes other than climbing trees (and not just in dinosaurs). I don't think we're far off the mark in this case, but until we find a fossil of one of the little blighters with its foot wrapped round a ginkgo branch or somesuch, we have to be cautious. Also, Microraptor is still (if my memory serves me correctly) the only likely example of arboreality among the Deinonychosauria, and is phylogenetically no closer to Archaeopteryx and true birds than any other taxon among the dromaeosaurs & troodontids (I'm working with Hwang et al 2002, Am.Mus.Novit, here). All the other well-known deinonychosaur taxa give the appearance of being cursorial.

4) I don't think Lars or myself suggested that endothermy precluded either theory of bird flight origins. As I mentioned before, the traditional model (for a long time the only game in town, going back to Heilmann, 1926) invoked an ectothermic gliding origin for flight as Archaeopteryx was not then considered capable of active flapping. However, if bird-like theropods were endothermic, then that opens up the possibility of a fast-running, high-energy ground-up origin of flight. My above point about the prevalence of cursoriality in deinonychosaurs (and for that matter in theropods as a whole) then becomes suggestive. Your point about bats is not relevant as it is beyond doubt that their endothermy evolved long before their flight. The same cannot yet be said for birds (although the evidence is indeed persuasive).

5) I would take very serious issue with your description of Ruben and Feduccia as "disingenuous" or "dishonest". And you're right, I haven't "taken much time to learn of their tactics". They're not creationist fundies, so I don't feel the innate urge to tear them limb from limb. They are both respected evolutionary biologists and they publish in high-quality, peer-reviewed journals. If the views they hold are not in the majority, and may prove to be mistaken, then that is no crime. At the very least, the people who disagree with you keep you on your toes and force you to continually re-evaluate your assumptions. By playing devil's advocate they keep you honest and focused, and stimulate the scientific inquiry necessary to prove them wrong. They are not some blogging troll to be scorned.
In the case of Ruben, he is primarily a physiologist and so has a different perspective from a palaeontologist, as I mentioned in an earlier post. He gives less importance to bones than to soft-tissues when evaluating evidence for the physiology of extinct animals. His approach is instructive, important and - some would suggest - rather more rigorous than that employed by some palaeontologists. In my own sphere of nonmammalian therapsids he has made notable contributions.
Feduccia's main intellectual problem with the theropod ancestry of birds was (correct me if I'm wrong here) the issue of digit homology. His beef was a good and valid one, and it still is. It has been routinely whitewashed over by palaeontologists (who are too often geologists with little understanding of, or interest in, biological matters like embryology and physiology) and its potential resolution has required considerable re-alignment of our understanding of digit formation during embryogenesis. If Alan Feduccia hadn't kept banging that particular drum, the research necessary to prove him wrong might never have been done. And in any case, I look upon his tenacious clinging to an unpopular and anachronistic theory as very human. He's an old man, and scientists can remain very attached to the world-view that was prevalent in their youth. It's not commendable, but it's no reason to "get medieval on his ass", as I've seen said in other fora. I repeat, it does not make him a creationist troll. Being wrong is no crime.

6) Lastly, Greg Paul. I've enjoyed his books very much and I've been broadly accepting of what he says. Earlier you said that Paul "assumed" there were feathered theropods, now you say he "derives tentative conclusions". These are not the same thing. There are no prizes for predicting something which later turns out to be so. I could throw out ten predictions based on common sense alone - if one of them comes to pass that does not make me a prophet. In the case of feathered non-avian theropods, I think this was seriously on the cards since Ostrom's 1969 revision of Deinonychus. "Predicting what the fossil record will show" is a dangerous game to play, as one runs the real risk of interpreting new specimens through the blinkers of pre-existing interpretations of earlier data.
It's very difficult to be credible as a vertebrate palaeontologist if you're not employed by a university, a museum or a similar reputable institution, and (more importantly) if you're not publishing regularly in peer-reviewed journals. These are the foundations of professional science and are among the guarantees of our intellectual probity. We rightly berate creationist halfwits for not meeting these minimum standards of academic discourse. It's not good enough to "compare all ideas side by side" - if it hasn't been subjected to the scrutiny of your peers before publication, then I have a serious problem with it.
I hope PZ and readers will forgive me such a verbose post. I'm mercifully going to bed now as it's nearly 5 in the morning here.

"there's an Icelandic name if I ever heard one!"

Swedish. Icelandic would be Thórbersi Larsson, I think.

Lycaenops -
thanks for developing my off-the-cuff comment so thoroughly - you did a much more eloquent and complete job of it than I would have, even if I hadn't been busy with losing a credit card/packing/getting through airport security at 5:00 am/flying across the continent etc over the past 24 hrs.

Sorry about this guys
Lycaenops comments are numbered 1)2)3) ect... And my comments are found inbetween as well as "a. b. and c."

Lycaenops said:
Thank you very much for your comments. As I said earlier, I have no strong axe to grind on the origins of bird flight, but it would be remiss of me not to attempt to present a reasonably balanced view.
1) The flying capabilities of Microraptor are still a matter for debate. Given that there are no four-winged vertebrates alive today, we have no extant model for comparison which makes it particularly difficult. The best we can do will be to carry out a full biomechanical analysis involving computerised modelling. It takes years to do such things properly. "

So what? So is the flight ability of Archaeopteryx up for debate. The point is, Microraptors have just as much going for a volant life style based on its' osteology, as in most every traits used to imply flight for Archaeopteryx are also present in Microraptors...

2) I would contest your statement that Microraptor "shows all the same signs of being volant as Archaeopteryx". It has four wings, for a start, and the rest of its anatomy is distinctly different to reflect their apparently unique mode of flight. (I believe the possibility that one of the Archaeopteryx specimens has feathered hindlimbs has been mooted, but I don't think it's been published yet. I certainly don't remember seeing anything like them on the London holotype). In any event, we shouldn't expect Microraptor to fly like a bird, as it isn't a bird. It likely represents an independent origin of flight within theropods, which (I think) is far more exciting and provocative."

For one, why isn't a bird? Because you say so? Because someone has defined bird in some arbitrary way and decided Microraptors do not count as such? Who is this who has defined "Bird"? I certainly have not seen an accepted scientific definition of "Bird".
Also, what osteological difference limit Microraptor as a flier as compared to Archaeopteryx,...please, tell me?
How does having asymmetrical feathers on the hind limb prevent flight?
What modern bird does not fly but still has fully feathered wings which feathers are asymmetrical pinnate feathers?
What non-flight reason do birds use the asymmetrical aspect of its feathers for?
As for Microraptors being independant from Archaeopteryx, show me a closer anatomical match for Archaeopteryx within theropods, K?
Next, you have implied, by what you said above, that Archaeopteryx is not an independent lineage from birds. Show me how you've concluded this, and what non-arbitrary evidence includes Archaeopteryx, but not Microraptors in this conclusion?

3) There are anatomical correlates of arboreality but they are notoriously difficult to interpret. Sharp claws and grasping feet have almost certainly evolved on occasion for purposes other than climbing trees (and not just in dinosaurs). I don't think we're far off the mark in this case, but until we find a fossil of one of the little blighters with its foot wrapped round a ginkgo branch or somesuch, we have to be cautious. Also, Microraptor is still (if my memory serves me correctly) the only likely example of arboreality among the Deinonychosauria, and is phylogenetically no closer to Archaeopteryx and true birds than any other taxon among the dromaeosaurs & troodontids (I'm working with Hwang et al 2002, Am.Mus.Novit, here). All the other well-known deinonychosaur taxa give the appearance of being cursorial.

No closer, maybe, (but debatable for sure), but no further either, so why the separate lineage according to you? Why should Archaeopteryx not be placed directly within these groups rather than on the side?
Also, why are Archaeopteryx and Microraptors phalanges both slightly curved as we see in climbing primates?
Finally, no one doubts that, just as Ostriches are not arboreal, but robins are, that many deinonychosaurs were terrestrial. The fact that humans are terrestrial does not prohibit an arboreal past. The basic hypothesis across the board, that the theropods that did rise to flight would have been smaller and less likely found as fossils because of this, and that later forms that did go back to a terrestrial life would have become bigger, increasing their chance of preservation in the fossil record. The tree-down hypothesis that Paul states indicates that as we go back closer to the node, we would find smaller versions of the later deinonychosaurs (dromaeosaurs, Troodontids ect...Basically what Paul refers to as the "avepectorans") and that they would become more similar to Archaeopteryx, and the different related groups would start to converge more in general morphology". He also stated they would show more traits linked to flight than their later descendants, which is obviously implied.

4) I don't think Lars or myself suggested that endothermy precluded either theory of bird flight origins. As I mentioned before, the traditional model (for a long time the only game in town, going back to Heilmann, 1926) invoked an ectothermic gliding origin for flight as Archaeopteryx was not then considered capable of active flapping. However, if bird-like theropods were endothermic, then that opens up the possibility of a fast-running, high-energy ground-up origin of flight. My above point about the prevalence of cursoriality in deinonychosaurs (and for that matter in theropods as a whole) then becomes suggestive. Your point about bats is not relevant as it is beyond doubt that their endothermy evolved long before their flight. The same cannot yet be said for birds (although the evidence is indeed persuasive).

Again, so what? It was stated here that the fact that theropod dinosaurs can be considered to have developed air-sacs..hence probably endothermy, that this was a blow to a tree-down hypothesis. This is bullhookey and shows no signs of logic. You are simply pointing to a tree-down "model" (as in one version, but not the whole of the tree-down hypothesis models) that was developed in a time when it was generally assumed all theropod dinosaurs were cold-blooded, as well as their archosaurian relatives, which people like Heilmann believed were the actual common ancestors to both...
Later versions of tree-down vary quite a bit, and the more modern versions often have warm-blooded theropods as the ancestor, and not a cold-blooded animal. The best that could have been said is, if it is true that air-sacs developed first (as Paul has been saying since day one), and this indicated endothermy (again, as stated by people like Paul from day one), and that these same theropod dinosaurs gave rise to "birds", that the idea that flight stimulated the initial development of endothermy in birds, is false. It says NOTHING about whether or not flight evolved from the ground-up, or the trees-down. Owing to the fact that Paul had stated evidence for air-sacs in theropods, and believed this was an indication for endothermy in these same animals over 20 years ago, I hardly think this same evidence, that is completely consistent with his position from 20 years ago, can be seen as evidence against his same said postulation of tree-down origins of flight.

5) I would take very serious issue with your description of Ruben and Feduccia as "disingenuous" or "dishonest". And you're right, I haven't "taken much time to learn of their tactics". They're not creationist fundies, so I don't feel the innate urge to tear them limb from limb. They are both respected evolutionary biologists and they publish in high-quality, peer-reviewed journals. If the views they hold are not in the majority, and may prove to be mistaken, then that is no crime. At the very least, the people who disagree with you keep you on your toes and force you to continually re-evaluate your assumptions. By playing devil's advocate they keep you honest and focused, and stimulate the scientific inquiry necessary to prove them wrong. They are not some blogging troll to be scorned.

OK, so you care to defend them? OK then, defend these 3 positions as scientific for starters (I will add many more as you answer to these). I will start with Feduccia.
a. Feduccia has backed Larry Martin in the claim (and Published in a Book for the general public no less!) that the pretibial bone is not homologous to the ascending process in theropod dinosaurs due to the association of this bone with calcaneum in adult neognathus birds, and has used this as evidence against a dino-bird link. Their claim is that the ascending process of the astragalus in theropods is part of the astragalus, and not a separate bones fused to it during development (where is their theropodian embryonic evidence for this?), and they also claim embryonic evidence shows the pretibial bone to be a separate ossification in neognath birds which later fuses to the calcaneum, hence, not homologous to the theropod ascending process of the astragalus...
Now, at the same time, when Caudipteryx was found, and found with obvious pinnate feathers, instead of seeing this obvious theropod as a feathered theropod, or theropod/bird, they claimed it was a secondary flightless Enantiornithine bird with no relationship to theropods (again, despite the Osteological evidence to the contrary). What is the problem with this? Yep, you guessed it. The pretibial bone of Caudipteryx? It was exactly the same as seen in theropod dinosaurs. Did they now ignore the idea of the pretibial bone being evidence against a dino-bird relationship based on their previous reasoning? Or even, realize their confusion and realize Caudipteryx could not be bird based on their past reasoning? Nope. They still use BOTH lines of reasoning even though they are in direct conflict with one another. Where have we seen stuff like this before, hm? Creationists maybe?
(also, the last, and newest Archaeopteryx specimen to be described showed Archaeopteryx to be consistent with the theropod version of this trait as well, yet still no comment by Feduccia on this contradiction)

b. Next we see Feduccia claim that there wasn't a furcula in theropod dinosaurs (The Ol' Heilmann argument) when, of course we have known for a very long time that Oviraptors have had this structure (it is also odd that Oviraptors are extremely similar to Caudipteryx, but Feduccia claims Caudipteryx to be a secondary flightless bird, and Oviraptors to be totally unrelated theropods which was too anatomically different to have given rise to birds, but I digress). Now we have found this same structure we see in Archaeopteryx and modern birds in, not only animals like Microraptors, but extremely basal theropods related to Coelophysis (they are also found articulated if you were wondering).
How does Feduccia respond to these finds? Does he admit they have been found? Well, no actually, and here is his reasoning. Feduccia claims, the fused clavical--wishbones were evolved for flight, and these basal theropods do not fly, so despite any similarities in structure and articulation within theropods, they cannot be homologous structures. Now, if that isn't the circle reasoning of a creationist, I do not know what is. Now, care to defend that position of his? Does it have merit? Is it circular in reasoning? Is that the methodology of someone trying to follow the rules of evidence?

c. Feduccia, and friends, have been arguing for 30 plus years or so?...that dromaeosaurs, are theropod dinosaurs, and that these theropods, as in dromaeosaurs, are too anatomically different from birds to have given rise to them (and have you seen some of the animals he claimed were possible ancestors? Wow!). He argued this over and over again and has only become louder over time. But what about in the past several years, after obvious feathers are found over and over again on these animals from Places like China? Has he admitted that these animals had feathers? The answer is, YES!, he finally has. Now, without giving a single anatomical reason for, he has now decided these dromaeosaurs are not only related to birds, the ARE birds! Now, does this mean he accepts that dinosaurs gave rise to birds? Well, no actually. How is this so you might ask? Well it is gosh darn simple; he has decided that dromaeosaurs are not actually theropods. His anatomical reason for removing them from this groups? We are still waiting for it...
Still think the guy isn't disingenuous? A bit on the dishonest side maybe? Care to defend his actions, and or arguments here? I do not mean avoidance by saying, "He be published so he "Authority!!!". I mean get down into the actual issues of the debate and show me how he isn't being a complete spaz on the level of your average creationist?

5)... continued....In the case of Ruben, he is primarily a physiologist and so has a different perspective from a palaeontologist, as I mentioned in an earlier post. He gives less importance to bones than to soft-tissues when evaluating evidence for the physiology of extinct animals. His approach is instructive, important and - some would suggest - rather more rigorous than that employed by some palaeontologists. In my own sphere of nonmammalian therapsids he has made notable contributions.

I am going to deal with Feduccia first for space, and later we shall deal with Ruben and his mess.

5)...continued more: Feduccia's main intellectual problem with the theropod ancestry of birds was (correct me if I'm wrong here) the issue of digit homology. His beef was a good and valid one, and it still is. It has been routinely whitewashed over by palaeontologists (who are too often geologists with little understanding of, or interest in, biological matters like embryology and physiology) and its potential resolution has required considerable re-alignment of our understanding of digit formation during embryogenesis. If Alan Feduccia hadn't kept banging that particular drum, the research necessary to prove him wrong might never have been done. And in any case, I look upon his tenacious clinging to an unpopular and anachronistic theory as very human. He's an old man, and scientists can remain very attached to the world-view that was prevalent in their youth. It's not commendable, but it's no reason to "get medieval on his ass", as I've seen said in other fora. I repeat, it does not make him a creationist troll. Being wrong is no crime.

First you claim a whitewash over by the palaeo people, so I was going to go into this big long explanation of digit development and how it relates to this issue, and how what Feduccia claimed, was BS. Then I see that you admit that you already know Feduccia main argument, as in the digit primordia already has the adult identity set, has been shown to be false. So, how are we whitewashing here? Now, has Feduccia admitted to this in any way? Has he answered to it at all other than by putting his head in the sand in the hopes of the big bad theropod going away?

Yes..he is old, and that is no crime. Is he disingenuous with an eye more on his image than the rules of evidence and logical thinking? Hm, again...I wonder how he differs from your average creationist here?

6) Lastly, Greg Paul. I've enjoyed his books very much and I've been broadly accepting of what he says. Earlier you said that Paul "assumed" there were feathered theropods, now you say he "derives tentative conclusions".

Trying to play semantics?

6)...These are not the same thing.

Assumed as in, based on the evidence he saw, it implied to him that they had feathers. To be an assumption does not deny evidence helped lead us to the same said assumption. So no silly semantics please...

6) ...There are no prizes for predicting something which later turns out to be so. I could throw out ten predictions based on common sense alone - if one of them comes to pass that does not make me a prophet.

First, I never said the guy was a Prophet, stop implying hyperbole on my part that was not stated by me. Next, he didn't just make wild speculations (You claim you've read his books?) but derived his tentative conclusions based on what the evidence indicated to him.

6)...In the case of feathered non-avian theropods, I think this was seriously on the cards since Ostrom's 1969 revision of Deinonychus.

Paul predicted that animals like Compsognathus would most likely be feathered, and Ostrom denied this possibility. After finding Sinosauropteryx, which is generally placed under the family Coeluridae, and the sub-family Compsognathinae, we see feathers were found in these animals as Paul predicted. In other words, Paul was not just following what Ostrom said, but was thinking for himself, and again, he turned out to be correct here. In reality Paul's ideas were and are vastly different from what we saw from Ostrom.

6)..."Predicting what the fossil record will show" is a dangerous game to play, as one runs the real risk of interpreting new specimens through the blinkers of pre-existing interpretations of earlier data.

Paul has stated this as well, but if you are implying Paul has done this somewhere then show us where he has blinded himself as stated above. Since you're statement borders on an accusation, I think you owe that. It is like saying, "Girls that wear pants like that are generally tramps". In short, if you are calling the girl a tramp, then back it up or do not imply. I am backing up my comments about Feduccia, and will back up my comments on Ruben's when I am done with Fed.

6)...It's very difficult to be credible as a vertebrate palaeontologist if you're not employed by a university, a museum or a similar reputable institution, and (more importantly) if you're not publishing regularly in peer-reviewed journals. These are the foundations of professional science and are among the guarantees of our intellectual probity. We rightly berate creationist halfwits for not meeting these minimum standards of academic discourse. It's not good enough to "compare all ideas side by side" - if it hasn't been subjected to the scrutiny of your peers before publication, then I have a serious problem with it.

You cannot be serious here? You either understand the issues and follow the rules of evidence, or you don't. If Paul has an idea, he can publish it, and peers will review it then (and of course he has many people from the field view his works before time). If he has made a false claim then others are very free to point this out. We do not berate creationist because they publish with out letting someone see what they have written first. That is ridiculous. We berate them for their warping the truth, using semantics, giving half truths, quote mining, using tautologies, using strawman arguments, using non-sequiturs, being purely dogmatic and hundreds of other nasty things you have not shown Paul to be doing. I should also point out I have shown Feduccia to be using several of these ploys...

Now again, as I said from the beginning, there is no logical reason to state that, if we find air-sacs in more basal theropods, as in those less derived than the theropods believed to be close to the development of flight, that this is a blow to the idea that theropods/birds evolved flight from the trees down. Can this indicate the claim that theropods could not have evolved flight from the ground-up, due to ectothermy in theropods, to be false? Sure, but it is a neutral piece of evidence between the two and does not in any point towards one hypothesis verses the other...

hoo!
THAT was a thread-killer.
Truth is, we know almost nothing about dinosaur physiology that isn't highly debatable, and debated.
But it sure is fun to try to figure it out. Personally I think both Ruben et al. and Paul and his ilk have taken entrenched, too-extreme positions. A lot of what they both claim makes a lot of sense. See previous paragraph.
Feduccia, however, is a nut, imho.

Minor nit pick. You said, "and your muscles then compress the lungs, forcing the stale air out." That's only true during deep breathing. Muscles are not used for exhaling during normal tidal breathing. Elastic recoil of lung tissue is mostly responsible for exhalation when you are at rest.
http://www.meddean.luc.edu/lumen/MedEd/medicine/PULMONAR/apd/pp.htm

Combine this with the cool funky blood in Crocodillians and thier nice tricks with their hearts... we could create something cool...

Oh, yea... that would be bad... ;)

Cool! Thanks for your nice works. I think it would be hlpful to my research on Chinese alligators.

It is probably worth noting that small birds and mammals do not internally thermoregulate very well, compared to us, for example. If you disturb bats in a cool cave, you will see them shiver for several seconds before taking flight. Several times, in the early morning I have watched a roadrunner bird in the yard sunning with all feathers elevated and spred so as to get as much sun to the back skin as possible. They will hold this pose for several minutes if not disturbed.

I suppose the flow of blood in bird lungs is from front to back, a counter current system with the back to front airflow.

"It is probably worth noting that small birds and mammals do not internally thermoregulate very well, compared to us, for example."
Careful. The ability of bats and many (not all!) small mammals and birds to use hypothermia (and its extreme expression as "daily torpor") as an energy-saving strategy when inactive should not be confused with an inability to thermoregulate very well--this is a highly regulated and often facultative phenomenon.

"I suppose the flow of blood in bird lungs is from front to back, a counter current system with the back to front airflow."
Close, but not exactly; blood flow in bird lungs follows a "cross-current" pattern, not countercurrent, as illustrated about 4/5 of the way down the "fine class site" linked in PZ's original post.

It occurs to me that the existence of pneumaticized bones in nonavian dinosaurs does not really tell us about their lungs. The one-way lungs of birds could not possibly function without air sacs. Therefore airsacs had to exist before the one-way lungs. Ancestors of birds clearly had tidal lungs (as crocs and all other tetrapods still do), so there must have been archosaurs with both airsacs AND tidal lungs. The question is, which archosaurs?

Depends. As soon as air sacs and the connections between them are present, you have a flow-through lung, don't you?

The crosscurrent gas exchange is also found in crocodiles.

Pneumatic vertebrae are found in just about all adult saurischians, not just theropods. They are also found in pterosaurs.

I am now hooked on this blog after finding it whilst researching the paper you cited the information about the latex injected ducks from for a biology seminar. Amazing blog, great stuff, exactly what i look for in entertainment.
nicole.

Depends. As soon as air sacs and the connections between them are present, you have a flow-through lung, don't you?

The crosscurrent gas exchange is also found in crocodiles.

Pneumatic vertebrae are found in just about all adult saurischians, not just theropods. They are also found in pterosaurs.