• Category Archives Uncategorized
  • Study shows shunting in crocs is all about the acid

    Baby _C.palustris_ says:

    Yesterday a new study was released in the journal of Physiological and Biochemical Zoology. Researchers from the University of Utah, studied the effects of the well documented right-to-left shunt in crocodylians.Okay, let’s get the exposition out of the way first.

    Mammals and birds are both characterized by a 4 chambered heart. This heart allows the complete separation of oxygenated and deoxygenated blood streams. Less publicized, but equally as important, this separation also allows for a pressure differential to exist between the two ventricular chambers. That way the right – pulmonary side – of the heart can pump deoxygenated blood at low pressure to the delicate walls of the alveoli in the lungs, while the left – systemic side – of the heart, can pump oxygenated blood at much higher pressure (~7 times higher) to the entire body.

    Reptiles and amphibians differ from mammals and birds, in that they have a heart divided into 3 chambers (two atria, one ventricle). This allows for mixing of oxygenated and deoxygenated blood, which reduces aerobic efficiency.

    Please note the qualifier: aerobic.

    Now, as is often the case with herps, this is a rather broad generalization. The hearts of all reptiles, show various degrees of ventricular separation. Also, for all extant reptiles, there are physiological/haemodynamic mechanisms in place that reduce the amount of blood mixing. Meanwhile, some lizards (e.g. varanids), and snakes (e.g. pythons) have such a large muscular septum near the middle of their ventricle, that it actually completely separates the ventricle during the contractile phase (ventricular systole). Thus making varanids and various snakes, functionally four chambered. These reptiles are capable of producing pressures on their systemic side, that are 7 times higher than the pressures in their pulmonary side. In other words, their functional four chambered hearts allow for pressure differentials that are on par with mammals.

    Then there are the crocodylians. Crocs have the most complicated heart of any vertebrate. They are the only reptiles that have evolved a complete seperation of their ventricles. They are anatomically four chambered. Yet, they also retain the ability to mix their oxygenated and deoxygenated blood supplies. This is accomplished through a small connection between the right and left aortic arches (which come out of each respective ventricle). This connection is referred to as the foramen of Panizza. Making things more interesting still, croc hearts also feature a cog toothed valve that can completely block the flow of blood to the lungs, thus turning their hearts into a double pump systemic circuit.

    </exposition>

    So now we know the how it works, the question we want answered next is: why did it evolve in the first place? The classic “orthodox” explanation has been that all of these traits evolved to allow formerly land dwelling crocodyliformes stay underwater for long periods of time. A four chambered heart is great for aerobic endurance, but pretty darn useless for an animal that spends most of its time holding its breath. In that arena, a three chambered heart is a more efficient system. By mixing oxygenated and deoxygenated blood together, crocodylians and other reptiles are able to siphon as much oxygen as possible from their blood, and thus stay underwater longer.

    As I said, that was the old explanation. Now there is a new one:

    Farmer, C.G., Uriona, T.J., Olsen, D.B., Steenblick, M., Sanders, K. The Right-to-left Shunt of Crocodilians Serves Digestion. Physiological and Biochemical Zoology. Vol. 81(2): 125-137. doi: 10.1086/524150

    Farmer et al studied several groups of juvenile American alligators (Alligator mississippiensis). Each group underwent surgeries of various sorts to measure, and/or block the right to left shunt. The working hypothesis was that crocodylians use their right to left shunt, to serve digestion, by providing a greater reservoir of hydrogen ions (left over from the retention of CO2) for stomach acid secretion. It was suspected that if this was true, then one should see a greater degree of right to left shunting in animals that have just eaten.

    So what did they find?

    Well, for one, they found that juvenile alligators have a preferred postprandial body temperature of ~30?C, and will maintain that temperature to within .03?C. That’s a degree of temperature control worthy of any mammal, or bird.

    Another thing they learned was that alligators that were allowed to stay at that temperature, were a real bugger to keep under control. So they had to drop the temp down 3 degrees, to 27?C instead.

    Farmer et al learned that gastric acid secretion is temperature sensitive. Alligators produced greater quantities of gastric acid at 27?C, than at 19?C.

    Oh yeah, they also learned that crocodylians produced a tonne of acid. At maximum secretion, acid production was an order of magnitude greater than that measured in any mammal, or bird. For those keeping tally at home; that’s 10 times greater.

    The authours final observations warrant some thoughts.

    That the left aorta, which arises from the right – pulmonary – ventricle, is the main blood delivery route for the digestive system. During right to left shunting, oxygenated blood from the left ventricle, gets shoved to the left aorta, and down to the digestive system. That this coincides with increased gastric acid secretion is telling, and strongly suggestive as to the role of the R-L shunt.

    Yet R-L shunting also occurs during dives, and this is still the best explanation for the cog toothed valve. If the crocodylian heart really was specifically developed to increase digestion, then why block the path to the lungs at all? This study shows that the gastrointestinal system benefits from increased oxygen to these tissues. So why block the lungs, if one is trying to keep them oxygenated. Unfortunately the paper doesn’t really mention whether, or not the cog toothed valve was activated during this process. Personally, I don’t remember reading any case of the R-L shunt being used in crocs, without incorporating the cog tooth valve, so…

    I felt that the authours put too much emphasis on endothermy vs. ectothermy. Their final observations involved a blanket statement regarding the R-L shunt in all reptiles. As I mentioned above, crocodylians are unique in their cardiovascular anatomy and physiology. They are also renowned for their very acidic stomach acid. It would seem more parsimonious to say that the R-L shunt in crocodylians, plays a large role in gastric acid secretion for these animals only; and wait for subsequent studies in other reptiles before saying this is true for the whole class.


    Xenomorph
    Okay, so maybe their acid isn’t quite this strong, but you get the point.

    Lastly (I know, I know, this just keeps going), I found it interesting that they studied the effects of gastric acid secretion on the vertebra of a cow. This vert took over 2 weeks to digest! While I can accept that this was partly due to the size of the object, and it’s material (bone is tough, after all.), but 2 weeks! Even at the lower temperature that the experimental group was kept at, it seems hard to believe. The authours gave no mention of gizzard usage in these animals, which suggests that the animals were never given access to gastroliths, which should have sped up the digestive process considerably.

    Either way, the study was interesting. I just think that the authours took their final results a little too far.

    ~ Jura


  • Argh

    No sooner do I update my WordPress version; a new one comes out. Oh well, now that I know how to do it, things should at least go a whole lot faster.

    I’ll probably do the switch tonight so I no longer have to get constantly bugged about needing to update.

    ~Jura

    ————————

    Update: Well, as expected, that went easily. Everything is (once again) up to date.


  • Life in Cold Blood

    Life in Cold Blood

    I just found out that David Attenborough’s latest (and possibly greatest) documentary series: Life in Cold Blood is now out on BBC One.

    I remember talking to a fellow who was working on this series, about 2 years back. At the time, he mentioned that the goal was to portray reptiles doing things no one had ever seen before. It sounded great, and now I’m looking forward to seeing how successful it was in its portrayals.

    Unfortunately, as a citizen of the U.S., I’m going to have to wait until it gets released on DVD here, much like Planet Earth, or Life in the Undergrowth…or Blue Planet: Seas of Life…or…you get the point.

    Damn you BBC. Why do you have to make such enticing programming. >:)

    Anyway, for those in the same boat as me, make sure to visit the official site. It features clips and interesting behind the scenes shots. We might not be able to watch it yet, but we can at least whet our appetites.

    ~ Jura


  • The New Mexico plagiarism debacle.

    Faux NMMNHS bulletin

    To kick off day two of this 30 day romp, I thought it would be pertinent to write about the whole NM aetosaur “who named what, first” drama. For those who haven’t been following what’s been going on; Nature ran a news article a few days ago that brought to light the apparent seedy practices going on at the New Mexico Museum of Natural History and Science. Though Nature’s article only recently brought this to the public’s attention, this practice had been known of and talked about for almost 2 years now.Paleontologist, Mike Taylor, along with grad student Jeff Martz of Texas Tech, and William Parker of Petrified National Forest, Arizona, have found themselves at the heart of a drama they never intended to get in. As documented on his site, the folks at the NMMNHS (in particular: Dr. Spencer Lucas), have apparently been stealing the hard earned work of others, in an effort to pad their own resumes. It has been mentioned (anecdotally) that Dr. Lucas had made a personal goal of publishing more papers than Edward Drinker Cope (who currently holds “the record” at 1200). In my mind, this is an honorable goal to reach for, but if it means cutting corners and releasing work that is either not publish worthy, or outright stolen, then it seems to defeat the purpose. In science, quantity of published work is a distant second to its quality.

    So, did Lucas and company do this on purpose, or was this just a glaring oversight on their part? Were they just being overzealous? To date, that question remains unanswered. Still, it is telling that Lucas and co have yet to respond to Mike, Jeff, Bill, Matt or Darren. The only official response has been from the first (and currently only) mass media mention of this (one has to sit through a quick commercial to read the article). In the article, Lucas denies any wrongdoing.

    Even more disturbing, especially in terms of future ramifications, is the fact that Spencer Lucas is one of the editors on the NMMNHS bulletin; a forum that he uses a lot to publish his findings. In the land of academia, this is a big no no. By submitting official technical papers to a journal that he has some (if not all) content control of, Lucas is able to bypass a portion of the peer review process (basically, the final say on whether or not a paper gets published at all), and pump papers out way faster than average. That isn’t to say that Spencer Lucas and his colleagues at the NMMNHS are using the bulletin for this purpose. This investigation is still in its infancy, so I’m reserving final judgment until then.

    That said, all the accumulated evidence so far (including anecdotal statement from folks who have worked around Dr. Lucas) seems pretty damning. At the very least, it looks to make the NMMNHS bulletin no longer a peer reviewed (and thus respectable) body of work.

    There is not much more that I can add here that hasn’t been documented far better on Mike Taylor’s, or Darren Naish’s respective websites.

    What I will say, is that having spent a fair amount of time in the state of New Mexico, I am not surprised to see that Mike and co. are having as rough a time as they are in trying to seek retribution. New Mexico bureaucrats have a tendency to “protect their own.” If one is a local, or close enough to it (i.e. one has lived their for 10 years, or more, and has established a good reputation with the locals), then one is given free rein to do whatever the heck one feels like, without worry of getting caught. This has allowed many folks to get away with everything from bribing local food inspectors, hiring illegal immigrants, dealing drugs out of the back of the local convenience store and so forth.

    Shaffer Hotel
    The Shaffer Hotel. Once owned by a lady whose blatant mishandling of money resulted in the IRS taking the property away. She was later given a job at one of the local banks!

    It doesn’t help that the state is fairly desperate for attention. Having the chance to boast about having a scientist who has published the most papers of any other scientists in the world, or housing a bulletin that sees the largest growth in published work of any other journal in the country, is just the kind of thing that would cause folks in the political arena to overlook the ethical ramifications, in favour of bragging rights. After all, these are the same people who gave us the Albuquerque Isotopes.

    Finally, I find it disappointing that in a year’s time, aetosaurs, which were these awesome crurotarsan beasts, will now be known mostly for this whole debacle.

    Maybe someone can do a documentary about these guys, to help with their PR.


  • 30 Days

    30 Days

    Okay, so I originally intended this to start on February 1st, but I wanted to get WordPress updated first. Having surfed internet, and dealt with web design for over a decade now, I’ve had the opportunity to watch as fads come and go. I’ve also had the chance to see exactly what it is that creates a following. In the case of blogs, webcomics and podcasts, content may be key, but consistency is just as important. One can have the most amazing blog in the world, but if it is only updated once a year, then there won’t be much of a following behind it.This brings me to my site. The rate at which I’m putting up new content is just this shy of pathetic (I do have many more reptile pages in the works, I’m just short of pictures, design and time). The blog/what’s new is doing pretty well though. Last week I decided that one thing I could do to help the site, would be to post more often. The problem I have is that, contrary to what the length of these contributions would assume, I really don’t have much to talk about. This makes it hard for me to want to log on and make a post.In other words it’s writer’s block.

    So I thought that the best way for me to overcome this writer’s block and get this blog really up and running, is if I presented a challenge to myself. In this case, the challenge is simple:

    “Spend 30 days writing at least one post per day.”

    So I’m going to give it a shot. From today, the 3rd of February, to 3rd March, I will be posting something new every day. It might be a short “meh” post, or a series of titanic rants about Cheetos, or something. Either way, there will be at least one new thing here during this time span. Hopefully by the end of the run, I will have gotten used to daily writing, and this whole blogging idea will become a little more palatable for me.

    So stay tuned. There’s more to come.

    ~Jura


  • WordPress update

    I finally got around to updating WordPress to the latest version. It was a little nail-biting at first. I followed the upgrade steps meticulously. After a couple of steps, though, I realized that this is actually pretty stupid easy. The entire process took about 10 minutes (most of that was waiting for things to delete, or upload).

    As is typical, not much has changed on the outset. The backroom is nicer though. It’s easier to add tags, and there is now a tab that lets me switch between the visual layout, and the more useful code layout (very helpful for removing the bloat code that wordpress likes to stick in all the posts).

    Anyway, there you go. Just a minor update to the site, and mostly for my benefit.

    ~Jura


  • Gharials dying

    _Gavialis gangeticus_

    Gharials are dying from a mysterious disease.

    I have been meaning to talk a bit about this one for a few days now. Getting around to doing this blog has been a bit of a hassle for me. I’m still not quite used to the whole “update often” format.Anywho, it appears that a group of gharials in a river sanctuary in India were dying from some enigmatic disease. Whatever the pathogen was/is, it appears to affect the liver and kidneys. So, the pathogen seems blood based then. Current thoughts seem to focus on pollution from the nearby Yamuna river. The animals may have eaten some badly contaminated fish.The end result has been the unfortunate demise of 50 animals so far. Given the critically endangered status of Gavialis gangeticus (they only live in India), setbacks like these are always a big deal. Hopefully this will turn out to be a localized event, and not a contagion.

    ~ Jura


  • Saw Cloverfield

    Cloverfield rocked

    So did it live up to the hype? In my opinion: yes.

    Early on during the marketing for the film, there was some worry that this might wind up like Snakes on a Plane and just end up biting its own tail. Thankfully that never happened.

    The goal for this review is to keep things spoiler free. Part of the fun of Cloverfield is in maintaining the mystery. With that said, let’s see what I can report.

    For starters, this is the only film I’ve been to that had a warning placed in the theatre. The warning stated that due to the nature of the cinematography, there was a chance that people could suffer motion sickness. The movie folks aren’t kidding either. There was a lot of shaky cam in this film. Some of the shakes in the beginning came off very fake (it’s like they gave the camera to a monkey. Perhaps a drunk monkey). Those were by far the worst. After that, the cinematography became a lot more realistic and tolerable. Thankfully this film runs only 80 minutes long, so one does not have to require a stomach of steel to make it through. Which is not to say that I ever felt sick during the film (unsettled at times, but never sick). Then again, I can play first person shooters with no problem too; so there.

    I had no complaints with the actors. They played their parts well. No one was really memorable, but then they weren’t the “star” of the film anyway, so it didn’t really matter. J.J. Abrams and his crew made a point of keeping the witty one liners down to a minimum. While some people might argue the believability of the choices that some of the characters made, I didn’t really see the main characters do anything that I wouldn’t have done in that same situation. Cloverfield also had some of the most realistic military I’d ever seen in a giant monster movie (not a high bar, I know). The military personnel actively tried to help people, and never tried to stifle information about the monster, or what their plans were. That was a nice change of pace from the more X-Files centric view that tends to pervade these movies.

    So what of the crux of the film? How did the “star” pan out?

    I have to say; I really enjoyed the look and feel of this monster. I don’t want to give away what it looked like, but I will say that Cthulhu fans and Silent Hill fans should be pleased. The beast gave off a menacing, surreal aura, whilst emitting these haunting sounds as it moved about. This gave it a nice creepy presence that I have never felt with any other giant monster before.

    As for the shooting style, it’s a mixed bag for me. I like the approach that J.J. Abrams took with this film. That said, I don’t enjoy shaky cam “doc-style” at all. I find it annoying, and I believe it takes one out of the film because it makes a point of telling the audience that there is a camera man there. For Cloverfield, though, these complaints were moot. We know that there is a camera man in this film, so the “doc-style” made perfect sense. This was one of the very few times where I have found the shaky cam to actually add to the immersion of the film. Another plus to this style was that it forced all the special effects to be almost entirely background based. That is to say, there were very few set-up shots for the CG. This, in my opinion, made the effects all the more realistic. There were no scenes of people running to designated spots to look up at a creature that they knew was going to be drawn in later. Instead, we saw people going bat-shit crazy and the effects artists, having to subtly insert their effects within these sloppy camera sweeps. By doing this, the effects meshed with the film much better, and added to the sense of immersion. Two scenes particular really showed this off. One was on the Brooklyn bridge, while the other was on the street with the military. There was also a very memorable scene in the subways that not only felt real, but was genuinely creepy.

    As for complaints, I really don’t have much. Folks who are used to the classic storytelling formula will not be happy with how this film wraps up. The writers leave a lot of the film to audience imagination. I liked this approach. One of the problems with many of the movies out these days (especially in the action/horror/thriller genre) is that they explain too much. I hate it when movies talk down to me. Cloverfield never talked down to me. That isn’t to say that there weren’t some predictable moments in the film (e.g. the helicopter scene, or the nightvision scene), it’s just that the film never took a moment to pull me aside and explain the obvious. It never pulled out that one narrative tool that is almost always used…badly. You know the tool. The really annoying one that always feels out of place because so few writers can do it right.

    What was it again?

    Oh yeah, exposition!

    This was a film that was devoid of almost any exposition. There was a lot that was never explained. This was a good thing! There was no explanation behind the origin of this critter. There were no points in time when the military sat folks down to explain what they knew about it. For that, I am thankful. By not explaining as much as they did (or is that: didn’t?), one was forced to put much of the backstory together with one’s imagination.

    As strange as it sounds, this was a monster movie that might actually stimulate one’s brain. How neat is that?

    Now there were moments that almost took me out of the film. For starters, the story is told through a single camera. This camera is an amazing – near magical – piece of engineering. It got the crap beat out of it, and still it ran fine. Dust and debris had no effect on the sensors and the battery was stellar. This battery kept going throughout the entire film with nary a stutter. Besides the camera, I also had to work a bit to maintain my disbelief when it came to the cast of characters. It was genuinely hard to believe that a group of hapless folks stuck in Manhattan could run into so many close calls with a multi-story beast running amok. It would have been nice if the filmmakers decided to incorporate multiple videos scattered throughout Manhattan instead of relying on this single video. Then there was the scene involving a dangerously placed piece of rebar and the remarkable healing ability of one character. Finally, there was the opening scene. I get that the filmmakers needed to establish a sense of where we were, but the party scene went on for too long. Most of the folks one saw were extras, and even the main characters didn’t really matter much (they mostly just served to keep us grounded in the story).

    Short of these minor flaws, the movie was all that I had hoped it would be.

    So now we are left with the final question. Did J.J. Abrams and co. succeed in their attempt to revitalize the giant monster movie genre?

    I suppose that only the box office results will truly tell. In my opinion, though, it does. For the first time ever, we are given a “victim’s” point of view of what it would be like when a giant monster attacks. Forcing the effects team to work within the confines of a handycam was a brilliant choice, as it resulted in a much more realistic presentation of the CGI. I’m hoping other movie makers take note of this fact, and incorporate more subtle CG into their films, rather than the current gaudy style we’ve been seeing.

    Though it will never shake comparisons with Blair Witch, Cloverfield is nonetheless a successfully fresh new take on how to do a monster movie. I highly recommend this film to monster movie fans, horror fans and thriller fans alike. I also recommend it to anyone who enjoys it when movies shake up the tried and true blockbuster formula.

    Enough of my babbling, go see it.


  • “Dakota” and National Geographic

    This upcoming Sunday (9th December), National Geographic is going to be airing a special devoted to the dinosaurs (and other interesting critters) of the Junggar basin. The overall information conveyed should be interesting. The less than stellar CG models should not. Seriously, in the land of dino docs, National Geographic has got to have the smallest budget. Whatever though, it’s a documentary. The actual look shouldn’t matter all that much.

    That said, be prepared to hear a lot of nonsensical roaring. Oh, and seeing Guanlong with an idiotic mane.


    The second part of the special deals with a finding here in the states. A hadrosaur by the name of: Dakota. The species has yet to be worked out, but that’s not so important as the fossil itself. Dakota represents the most complete dinosaur ever.

    Think about that…ever.

    See Dakota is a mummy. Not the Egyptian kind (obviously), but the same basic premise. Basically this hadrosaur wound up getting buried in anoxic material faster than any bacteria had a chance to degrade it. Not only does Dakota preserve skin (which many other hadrosaur mummies have done), but it also preserved muscle tissue, and tendons. Who knows, there might even be some viscera in there.

    Everything is still pretty hush hush until after the NG special. All that’s really been released so far is that the evidence from the mummy shows that dinosaurs were much longer than previously thought, and that Dakota had a far more muscular hind end than anyone imagined. This extra muscle has been (speculatively) translated into faster running speed for hadrosaurs. The current media blitz has everyone believing that hadrosaurs could outrun Tyrannosaurus rex. To be honest, that is taking the speculation a bit too far. This data is interesting for what it tells us about hadrosaurs. It doesn’t really say much about T.rex.

    That said, I don’t really see a problem with the thought of hadrosaurs being faster. Despite what all the T.rex fanboys would have the world believe, T.rex was just another predator. Like most predators it probably had a kill ratio that was pathetically low (i.e. it lost most of what it hunted). There’s nothing wrong with that. Hadrosaurs evolved with tyrannosaurs throughout their geological history. If tyrannosaurs were so good that they “got one” every time, then it wouldn’t seem very likely that hadrosaurs would have lasted as long as they did.

    Plus, there were a whole lot of hadrosaurs back then.

    Anyway, this is my heads up for folks who don’t know. The air date is December 9th at 9 EST (8 C/P). That’s all American time. For the rest of the world, feel free to adjust GMT to your respective times.

    For more on the whole show, check out NG’s official site for it:

    Dino Death Trap


  • Intelligent Design on trial

    Science vs Religion Simpsons style
    As for science versus religion, I?m issuing a restraining order: Religion must stay 500 yards from science at all times.


    This is yet another case of me coming to the party a bit late. I can’t even blame my connection quandaries anymore, as I am now up and running 24/7. I guess I haven’t yet got the hang of this whole “blog” thing. Anyway, on Tuesday (13th Nov) NOVA aired their special on the infamous Dover case. They went over the causes that lead up to it, as well as what was at stake.Though I missed the chance to let folks know about this ahead of time, I can let you guys know that PBS has made the entire show available online.

    Just head to:

    http://www.pbs.org/wgbh/nova/id/program.html.

    The special is two hours long, and broken up into 12 chapters. Apparently the ID folks were not happy with the treatment that NOVA was going to give the special (i.e. an objective one), so few proponents agreed to be interviewed. That stance certainly isn’t going to do anything helpful for their cause.

    So if you are curious about the whole debate, or are active in it, check out the program. It’s worth watching.