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Teaser Post

Posted by tigerhawkvok on May 28, 2009 21:15 in biomechanics , sauropods , biology , research , paleontology

A teaser post ....

Suspension Model

Image from a preprint of my paper. CC-BY-NC-ND 3.0

VS

Neck held up

Copyright Taylor, Wedel, Naish 2009.

Via TetZoo and SV-POW. Amusingly, I know one of the authors personally, and I am really interested in what his feeling will be when my paper gets to review.

Nitrogenous Disposal

Posted by tigerhawkvok on May 23, 2009 02:30 in evolution , biology

Answering a call for a post on ureotelism vs. uricotelism, I thought I'd walk readers through a bit of phylogenetic bracketing that Kit, Rachael, and myself discussed a few nights ago while going through our habitual game of StarCraft.

< !-- SC pic -->

Vertebrates have three primary methods of disposing of nitrogenous waste: excreting ammonia, urea (ureotelism), and uric acid (uricotelism). Of course, all three have their own trade-offs. Excreting ammonia is highly efficient, uses few resources, and little energy, but needs to be done in large amounts of water to avoid toxicity. Of course, as life evolved in the oceans, this was not a problem, and excretion of ammonia is the ancestral/primitive state, exhibited by most actinopterygians (ray-finned fishes, like tuna), and many basal vertebrates. Modern sharks, amphiba and theria (amphibians and mammals), on the other hand, excrete urea, which is less toxic than ammonia, and more energetically favorable than uric acid. However, urea requires a fair amount of water to dissolve it, and uric acid, being virtually insoluble, can be excreted as a solid paste with little water waste.

< !-- uric acid photo -->

So, next follows the question of any self-respecting scientist: between ureotely and uricotely, which would be the derived state? Ureotely has the evidence in its favor urea being more energetically efficient and less toxic than uric acid; uricotely is more conservative with water. However, to believe ureotely is the derived state requires that it was developed convergently in (at least) lissamphibia and theria. It is reasonable for amphibians to be ureotelic, as it is less toxic and less likely to provide problems for thier highly permeable skins, and the excess water is not an issue, given their environmental restrictions. We can therefore postulate that ureotely might have also been favorable for basal tetrapods. How to check, though?

Well, we bracket this entire thing by checking the closest living outgroup to tetrapods -- non-tetrapod sarcopterygians. Doing a bit of research, it turns out that lungfishes (dipnoi) tend to excrete urea, and not uric acid. This then strongly suggests that uricotely is a novel innovation in sauropsida, evolved as a water-conserving mechanism, and what allows reptiles (including birds) to dominate arid environments.

< !-- Centered Tree -->
Uricotely tree

The phylogenetic evolution of traits assuming uricotely to be basal to ureotely

Ureotely tree

The phylogenetic evolution of traits assuming ureotely to be basal to uricotely. An alternative tree would have the only innovation prior to the chondrichtyes/osteicthyes split, with a reversion to ancestral behavior in actinopterygians.

Any other conclusion would require the novel invention of ureotely no less than four times, so the simplest, or most parsimonious, solution would be to have it be the primitive state. The water conservation afforded by uricotely presumably gave sauropsids a leg-up during the arid conditions of the late Permian (and possibly evolved then — I know of no research done in either direction), and thus gave the dinosaurs an advantage.

Dinosaur Proteins

Posted by tigerhawkvok on May 04, 2009 18:45 in dinosaurs , biology , paleontology

ResearchBlogging.org

So, a quick read over the Science news this week led to an interesting news brief (DOI: 10.1126/science.324_578) about a paper that expanded on the 2007 claim that T. rex collagens were recovered (DOI: 10.1126/science.1165069 ; 2007 article DOI: 10.1126/science.1137614). [Edit: And my lagging on my Nature RSS also shows that Nature also had a very similar report (DOI: 10.1038/news.2009.422) ]

Brachylophosaurus composite image

Composite picture of Brachylophosaurus. Color pictures from Wikipedia, reconstruction copyright Scott Hartman.

So, a refresher for those who don't remember: Back in 2007, Science published a paper that stated proteins from collagen fibers were recovered from a T. rex sample. While fascinating, the paper received much skepticism over the method, and this paper attempts to address that issue with a new genus and much more strictly controlled procedures.

By demineralizing the bone matrix of the fossil, and comparing it to a Struthio sample, the authors identified protein fragments with FESEM analysis and then checked for reactivity with antibodies to avian collagen I, ostrich whole bone extracts, and a specific epitope. The first two showed reactivity, but the last did not, indicated that this was either a novel epitope or simply not preserved. There were further antibody test against elastin, laminin, and hemoglobin (all associated with blood vessels), with were all also positive.

One of the more interesting points brought up in the article that wasn't really addressed in the news brief (though it certainly need much more research and a larger sample size) was that the antibodies (to ostrich bone extracts) used in the preparation to test binding to the proteins bound more strongly to the hadrosaur proteins than to G. gallus (chicken) proteins. If this result is consistent across more testing, it actually provides another reference point to the (uncontroversial) status of Paleognathene birds being basal to Neognathae.

Another big issue with the 2007 paper was the mass spectrometry. Its results were considered to be possibly contaminated with bacteria, and too close to noise level. In this experiment, the machine used was more sensitive, and analysed at two labs. The authors still found collagen peptide sequences.

< !-- Clade Image --> Cladogram from the paper

Cladogram from the paper. Copyright the authors.

When phylogenies were inferred from the collagen sequences, the results were consistent with inferences based on genetics and the fossil record. The sampled onithodirans ended up collapsing into a three-way polytomy, with Brachylophosaurus and Tyrannosaurus resolving as related to each other closely, but the relationship between the non-avian dinosauria and the sampled neornithines remained unresolved. This problem remained even with the removal of T. rex from the phylogeny, still leaving a three-way polytomy. The authors point out that there was, for obvious reasons, a fairly low resolution in Dinosauria, but B. canadensis still resolved as a derived archosaurian, more closely related to birds than to Alligator.

< !-- Ideal Clade --> Ideal cladogram

The predicted clade, based on extensive fossil evidence.

Now, its important to note that though this is incredibly cool, this is a far cry from Jurassic Park. The proteins recovered from the collagen fragments are incomplete, and it is highly unlikely that even an egg of an ostrich would provide a suitable oocyte for cloning. That said, however, this certainly has the promise of making paleontology gain a genetic basis for phylogenetics to complement the fossil record. Though, as this study showed, there's a way to go yet.

As an aside, does anyone think it'd be useful for me to put in a DOI search box on the right hand panel?

Schweitzer, M., Zheng, W., Organ, C., Avci, R., Suo, Z., Freimark, L., Lebleu, V., Duncan, M., Vander Heiden, M., Neveu, J., Lane, W., Cottrell, J., Horner, J., Cantley, L., Kalluri, R., & Asara, J. (2009). Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. canadensis Science, 324 (5927), 626-631 DOI: 10.1126/science.1165069

Commentary on Sauropod Neck Posture

Posted by tigerhawkvok on April 30, 2009 00:24 in biomechanics , dinosaurs , sauropods , biology , paleontology

If you look at a (yikes! month old) Science "Letters", there an interesting, if brief, back-and-forth about sauropod neck posture between RS Seymour and PM Sander.

Up front, I'd like to say like Sander, I don't necessarily disagree with Seymour's conclusion; my own work (still undergoing revision that is halting its review process) strongly suggests that the necks were mostly held laterally, due to energetics and biomechanical concerns. However, I do take issue with the blanket scaling argument used on several points.

DSCF4647

Ara ararauna (Blue and yellow macaw), Hawaii

First, it is important to note that the work done by Seymour is based on mammalian modeling. I have no comment as to whether it strengthens or weakens his argument this way; however, as a saurischian dinosaur, a bird would be a much more convincing model point. Second, their morphology is wildely divergent even from birds, the closest living species to them. The anology, even to birds, would be as problematic for me as the biomechanical study that based T. rex on Gallus gallus (chicken). Merely being a close relative does not ensure analogy; the musculature distribution, posture, and body shape in both cases are significantly different from the model animal. The results might very well be interesting, but they are not sure be relevant at all.

While I also have some issue with the "plug and chug" nature of the blood pressure calculations, those you can't really get around — though I'd at least like to know if it was based on mammals or birds.

Well, that's my 2 cents for now. More later.

Amino Acids and Thermodynamics

Posted by tigerhawkvok on April 13, 2009 20:17 in evolution , physics , biology

ResearchBlogging.org

Now, this is pretty awesome — tying together biology and astronomy in one fell swoop. It turns out that the ten most common (of 20) amino acids are substantially more thermodynamically favorable to form. Now, that's certainly got to take a bit of wind out of creationist sails.

Abstract:

Amino Acid

An amino acid. R represents a functional group. Shamelessly hotlinked from Wikipedia

Of the twenty amino acids used in proteins, ten were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth via meteorites. We combine observational and experimental data of amino acid frequencies formed by these diverse mechanisms and show that, regardless of the source, these ten early amino acids can be ranked in order of decreasing abundance in prebiotic contexts. This order can be predicted by thermodynamics. The relative abundances of the early amino acids were most likely reflected in the composition of the first proteins at the time the genetic code originated. The remaining amino acids were incorporated into proteins after pathways for their biochemical synthesis evolved. This is consistent with theories of the evolution of the genetic code by stepwise addition of new amino acids. These are hints that key aspects of early biochemistry may be universal.

The results here hinge on the fact that the ranked amino acid frequencies under various criterion correlate strongly (r=0.96) to ΔGsurf, where ΔG is the Gibbs free energy, which is defined as:

Gibbs Free Energy

Source: Kittel & Kroemer 1980

Which is essentially the enthalpy of a system (loosely, the "thermodynamic potential energy") minus the fundamental entropy of a system

Entropy

Source: Kittel & Kroemer 1980. g(N,U) is more commonly known as the "number of accessible microstates", and is sometimes denoted as W

multiplied by the fundamental temperature (the temperature in Kelvin times Boltzmann's Constant, 1.381 x 10-23 JK-1). In essense, the "sign" of this value (and its magnitude) denote how easy it is for them to spontaneously form. The lower the free energy, the less energy is needed to make a given event occur; thus, something with a negative free energy is spontaneous and releases energy upon its occurance, such as dissolving NaOH in water. Some other events take energy to occur, such as dissolving CaCl2 in water. Thus, in the first example, the beaker gets very hot, and in the second, it gets very cold. So, under the premise of the abiotic origin of life, one would expect the most "entrenched", or common, amino acids should be the easiest to produce. The results from the research support this conclusion:

Group Gsurf (kJ/mol) Err MW (Da) Err ATP cost Err
Early Group 169.342.0 116.220.6 18.56.9
Late Group 285.094.1 157.323.2 36.217.3

Table of values for early and late group amino acids. All errors +/-.

Clearly, the "early group" amino acids, the ones most common in organisms, and that are most simple to form abiotically, have a formation advantage in terms of energy, size, and spontaneity over other amino acids. This is further supported (with some caveats expressed in the paper) in that the amino acid distributions were a bit off for hyperthermophillic bacteria — i.e., the ones living around underwater hydrothermal vents. With the higher energy densities available, differences in amino acid synthesis costs may be a reason for different amino acid preferences in high-expression proteins (though the authors are quick to point out this may merely be an artifact of high temperature stability for proteins).

The remainder of the paper is also quite interesting, but requires a bit more knowledge of biochemistry than I'd like to assume for this blog. The authors touch on the diversity of amino acids, and why the observed diversity in nature is fewer than the maximum number.

Hmmm. A spurt of posting might be coming ...

Paul G. Higgs, Ralph E. Pudritz (2009). A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code Astrobiology DOI: arXiv:0904.0402v1

Engineered Bacteriophages

Posted by tigerhawkvok on March 14, 2009 01:52 in biology , medicine

Some quick updates on last week's Nature:

Scientists are coming up with a novel way to fight bacterial infections in light of antibiotic resistant strains of bacteria, such as MRSA: make viruses do the work for you. By engineering viruses to weaken bacteria, antibiotics become more effective. The trick is, actually not to kill the bacteria. If you kill the bacteria, selection works too strongly, and you have bacteria that become resistant to the viruses. Instead, by making the bacteria weaker, you need bacteria to survive a one-two punch: supression of lexA3 (renders bacteria unable to repair DNA as well) and drugs (particularly of the sort that damages DNA).

MRSA comic.  Source unspecified.

The catch? You need to engineer a bacteriophage that is very specific, down to strain. Unless entire cocktails can be manufactured, strain-specific identification is required.

Lets see if a bit on Higgs gets posted tonight, or if I'm lazy and go watch Dollhouse.

Evolution and Language

Posted by tigerhawkvok on March 04, 2009 02:37 in General , evolution , biology

I still have my science posts planned, but I want to spend a moment to comment on biology terminology in the public sphere. I thus give you this declaration:

The use of "descended from" is a subtle, but constant linguistic method of undermining evolutoin and unecessarily seperating species.

What? That sounds high, mighty, obscure and arrogant. However, I think it's true. What of the supposedly innocuous statement: "Humans descended from apes". This has the implicit statement: "Humans are not apes". This enables people to say "We're not monkeys!" Or, "We have ape-like ancestors". This is like saying, "We have primate-like ancestors". Its just as ludricous. We do have primate-like ancestors, and ape-like ancestors, but those are outside of the appropriate splits. For something to be ape-like, it must be more basal than the last common ancestor between apes and its most closely related living organism. Using the terminology any other way is disingenuous and misleading. Thus, a predecessor to the first primate (depends on how you define things) might be primate-like; but using "ape-like" for a human ancestor is just as deceptive as saying an aye-aye is primate-like while inside of primates.

No, ape-like would have to be non-hominoid Catarrhinid, of which the living form most closely fitting that description would be a gibbon.

So, perhaps that was a bit abstract and focused on hominds. But, consider birds. Saying "birds descended from dinosaurs" is also deceptive. Birds are dinosaurs. We've found non-avian dinosaurs with feathers, long before flight showed up. Sheep and cow are both artiodactyls, saying they "decended from" artiodactyls clearly implies that they are no longer a member of that group. Similar things to this lead to the sloppy use of the word "amphibian".

Amphibian is used in three ways: meaning living amphibiously, in both water and land; meaning being a member of lissamphibia, and this blurry realm of amphibious tetrapods that had not yet broken into the great amniote/lissamphibian split. They are more accurately called "basal tetrapods", or "early amphibious tetrapods" -- but saying "amphibians" is poor word choice.

What this rant serves the purpose of doing is simply to say — watch your language. Watch your terminology. All of us, simply by watching our language, can have an impact and help spread awareness.

Thus end your 2am lecture! Tomorrow: Kepler and my involvment with it.

Bush ESA midnight legislation suspended

Posted by tigerhawkvok on March 03, 2009 18:29 in biology , news

Via the EBV blog: Bush's midnight legislation that weakened the act by not requiring scientist input (via the US Fish and Wildlife service) before federal officials could say a species did not need protection. This was, in fact, serious enough that California sued to prevent this.

Formally speaking, Obama suspended the legislation to review "whether it promotes 'the purposes of the [Endangered Species Act]'". This is certainly good news, and good precedent, for requiring scientific review!

I had started a post on salamanders, but the spazzy laptop ended up killing it. Oh well. That post, and the others I mentioned, will be up soon enough. Perhaps if everything works out right, tomorrow will be a small photoblog. Meanwhile, I'll leave you with an interesting link, via Grrlscientist over at ScienceBlogs. Hint: What's the last color you'd expect to see on a dolphin?

Ratites

Posted by tigerhawkvok on February 23, 2009 18:04 in biology , research

I've become increasingly interested in birds — particularly ratites — as of late. Posts like this over at TetZoo just make me more interested. Their evolution and morphology is fascinating, as well as the divergence in the group.

I wonder how much of this has to do with the unusually saurian characteristics of ratites (even the mammal-like kiwi)? I wish I would just pick something to be interested in and stick to it! My current list of "I'd like to do research in this some time" fields include:

  • Galactic evolution
  • Ratites
  • Stellar magnetograms on surface microstructure
  • Saurischian biomechanics
  • Compact object dynamics
  • Sauropsid evolution

Oy.

Fun fact for everyone: Did you know ostriches have the best feed:weight-gain ratio among land animals? They're actually by far the most efficient source of meat, as well as being rather healthy apparently. I'd like to try some ....

Velociraptor wrists

Posted by tigerhawkvok on February 19, 2009 02:49 in biomechanics , dinosaurs , biology , paleontology

The promised science post!

Rewatching Jurassic Park, I wanted to correct a rather small, but important and understated error.

There's a hint in the URL, of course. The answer? The claws — they're held horribly, horribly wrong.

Jurassic Park Velociraptors are named after Velociraptor mongoliensis, and modeled after a hybrid between the genera Deinonychus and Utahraptor. At the time the novel was written, there was some talk of moving Deinonychus into the genus Velociraptor, which was the convention followed by Micheal Crichton, though this didn't play out. However, all of these were dromaeosaurids, which are eumaniraptorans. In fact, Dromaeosauridae is the group closest to but outside of Aves. So, all members of eumaniraptora have a synapomorphy list that includes a "semilunate carpal".

Sinoris manus

Sinornis santensis manus

Tanycolagreus manus

Tanycolagreus topwilsoni manus. Scale in cm.

Cathayornis manus

Cathayornis sanctis manus.

All three of the pictures above show this semilunate carpal in other maniraptorans. Unlike most mammalian wrists, it cannot flex perpendicular to the radius-ulna plane (ie, what we would most commonly accept as perpendicular to the groud). Instead, its motions were restricted to that plane, giving a jacknifing motion, much like a flight stroke. This was an optimal grasping motion for prey, and good for grappling large prey, and was easy to adapt into a flight stroke (particularly given the presence of primary feathers on some dromaeosaurids).

Sadly, this does mean that the raptors couldn't open doors. They would have broken their wrists trying to make the motion!

Image citations:

  • Carpenter K., Miles C., Cloward K. New Small Theropod from the Upper Jurassic Morrison Formation of Wyoming. In "The Carnivorous Dinosaurs" (ed. Kenneth Carpenter), 2005.
  • Sereno PC., Chenggang R., Jianjun L. Sinornis santensis (Aves: Enantiornithes) from the Early Cretaceous of Northeastern China. In "Mesozoic Birds: Above the Heads of Dinosaurs" (ed. Luis M. Chiappe and Lawrence M. Witmer), 2002.
  • Zhonghe Z. and Lianhai H. Mesozoic Birds in China. In "Mesozoic Birds: Above the Heads of Dinosaurs" (ed. Luis M. Chiappe and Lawrence M. Witmer), 2002.

Enter Titanoboa

Posted by tigerhawkvok on February 07, 2009 15:45 in biology , news

A riddle: what happens when you cross a snake with a bus? Answer: A 13 m snake.

Scientists recently found Titanoboa, a 13 m boid from the Paleocene neotropical region (S America and S Asia). This thing was impressive; the animal probably had a 2m girth, weighed over a metric ton, and could eat a full-grown cow. As a member of Boidae, it was a full-on constrictor (which kind of begs the question of what it was constricting!)

Titanoboa

Probably the most interesting thing about it, though, is what scientists have done with the find. Using it, they have been able to estimate the neotropical region temperatures to be around 30-34 C (given the standard laundry list of assumptions). A Nature press release has more, with the primary article linked at the bottom (doi:10.1038/nature07671). Pharyngula has a research blogging post on it and some more pictures from the article.

I'm going to try to find time to read the paper — from what I understand, they just used a growth curve using modern snakes as a baseline, but I'm curious as to if they took into account some pythonine snakes can be facultatively endothermic (DOI: 10.1016/S0306-4565(02)00048-7 ). Granted, this has only been observed in pythonine snakes, but I wouldn't rule out convergency (though this has a high metabolic cost, this could considerably broaden the temperature range it could live in). I'd also be curious to see if oxygen isotopic analysis, such as done with theropod dinosaurs, can confirm internal thermoregulation (DOI: 10.1130/0091-7613(2000)28<799>2.0.CO;2).

That's it for now!

Polar Bear Queries

Posted by tigerhawkvok on December 26, 2008 23:26 in General , biology

So, I've been thinking a lot about polar bears.

It seems to me that the reduction in artic ice admits a few hypothesis:

  1. Less ice should result in worse hunting opportunities; as a corollary, this should result in longer periods between hunts / reduced success. This is born out by average polar bear mass decreasing in the past 50 years.
  2. Less ice at the poles should result in the bears moving to glaciated landmasses, where land is more reliable. This should predict increased measured population counted in North America, most notably AK
  3. Increased technology, including but not limited to radio tagging and sattelite imagery, should increase percentage of population counted during census
  4. As a result of items 1-3, there should be a dramatic increase in population count of polar bears

As a result, I'm not sure how reliable the idea that "polar bear population has increased" actually is. I would expect that. What I'm much more interested in is the actual population fluctuation. I think that taking a census on a similar species and comparing it to old data might be informative. For example, if a census of, say, Arctic Foxes were taken, and they were found to increase by a factor of eight over 1950s census, we might expect a similar jump in population among polar bears, which was not found, thus leading one to expect a practical decline despite observational increases.

While foxes are a bad example, I think it gets the idea across. The problem is finding a comparable model to compare polar bears to; something else that would have been forced southerly that is carnivorous. An alternate confirmation method would be to make population adjustments to match predator:prey biomass ratios for the observed alternate species (say, foxes:rabbits in this case), and scale it to polar bears.

I'm really interested in the result of this. My bet is on polar bear count falling rather seroiusly. As a K-selected top carnivor, nothing else makes sense.

Does anyone who reads this know how biology population census for species account for updated trackign methods?

Update and Shell-less turtles

Posted by tigerhawkvok on November 29, 2008 20:59 in evolution , biology , news , paleontology

Hm, I've not blogged in a bit. Well, I'm working on the graduate school apps with a bit of a mix of physics, astrophysics, paleontology and biomechanics. Some dual applications, some single. We'll see how it plays out.

I've also finally submitted my paper to Proceedings B, and hopefully it will be accepted (or conditionally accepted).

Nah, the real trick is money. The economy sucks, finding a job has been hard, and well, not quite enough money to make rent. Ugh. Well, perhaps I'll blog on science tomorrow at the airport. In particular, Science and Nature have had a few interesting articles as of late, such as one on a new turtle find -- it has a plastron, but no upper shell -- and with teeth! Dubbed Odontochelys, it is placed phylogentically basal to all all extant and extinct testudines. While I find the use of "Ontology recapitulates phylogeny" a bit problematic, its still a very interesting read, and I feel that its sparing use in this context is justified.

Odontochelys

It seems I blogged on science accidentally anyway. Huh. Perhaps not much, but nevertheless.

The full paper can be found here: Nature.com (DOI: 10.1038/456450a , Reisz & Head ).

Update 03/15/09: Link repair

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