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


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.

Tuesday Tetrapod: Gopherus agassizii

Posted by tigerhawkvok on May 26, 2009 21:32 in tuesday tetrapod

A quick one today — an threatened herp from right here in California, Gopherus agassizii.


G. agassizii, from Death Valley, CA

They can survive very long times (up to one year) without access to liquid water. The desert tortoise is classified IUCN "Vulnerable", almost strictly due to human interference (habitat destruction, invasive plants, etc). They are illegal to handle or collect in the wild.

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.

On Computers

Posted by tigerhawkvok on May 22, 2009 20:41 in computers

First, Liz's replacement:

An Eee PC 701, which I've had about a month now, running linux. Itty bitty, but nice an mobile, with a good battery life, It supplements Athena nicely. I've named it Nike, after the Greek goddess of victory.

Now, regarding my previous post on Windows 7, there were a number of issues with my graphics, but I had assumed it was a bad VRAM sector. Turns out, upon opening up the computer, my Koolance GPU cooling block was leaking.

Of course, it was out of warranty (an I hereby remove blame from ASUS and ATi for the failure). For now Athena is running open, with the block leaking into a bowl. I suspect large liquid pooling was avoided by the orientation of the cooler and the heat of the GPU. The new ATi 4850 (512 MiB, Sapphire) runs beautifully, and my current system specs give this ratnig:

< !-- System Rating -->

There is a weir problem with my system reporting 8 gigs but only addressing 6 — I might have to switch up the slots for the most recently added bit of RAM. So, this weekend I'm going to try to drain my system an replace my GPU block with my second CPU block (for my as-yet unpurchased second CPU). We'll see how it goes. Hopefully no insane hardware failures!

When I get to my desktop, I will replace the huge jpgs with something a bit more reasonable.

Tuesday Tetrapod: Struthio camelus

Posted by tigerhawkvok on May 19, 2009 04:04 in tuesday tetrapod

This tetrapod needs little introduction — Struthio camelus, or the ostrich.


S. camelus, the ostrich. Photographed at the Honolulu Zoo, Hawai'i.

< !-- Ratites --> The largest living bird, Ratites were once a much more diverse group, including the moas. Interesting, this does not include the "Terror birds" (Phorusrhacidae), which were more closely related to falcons and such. Generally their wings are strongly reduced, terminating in a single large claw hidden beneath their feathers. You can see a good emu deconstruction over at TetZoo.

Evolution of Novel Traits

Posted by tigerhawkvok on May 18, 2009 13:32 in General , evolution

Non Sequitur

Image hotlinked until I update this post from Berkeley

Yes, this ResearchBlogging entry on Panda's Thumb is almost a year old, but I still think it is a great article about a fantastic paper. Essentially, a group of E. coli developed the novel ability to metabolize citrate (Cit+) based on a potentiating mutation earlier in its evolution. Take that, creationists.

Prompted by Pharyngula posts and a high rate of creationist stuff recently. Off to the Burbank Airport to go back to Berkeley ...

On Fixing Computers

Posted by tigerhawkvok on May 15, 2009 20:56 in computers

So, I'm temporarily down from Berkeley in Glendale, and, as the life goes for the computer nerd of a family, it's time to take a look at the computers. As I wait for them to crawl their way into the next update or remove the next piece of crapware, I thought I'd post an article on some computing tools and practices for Windows.


Tuesday Tetrapod: Ambystoma macrodactylum

Posted by tigerhawkvok on May 11, 2009 23:37 in tuesday tetrapod

This Tuesday, we have a member of caudata (salamanders): Ambystoma macrodactylum.


A. macrodactylum, the long-toed salamaner. Found near Lake Tahoe, CA

Ranging from roughtly 4-9 cm, I strongly suspect this specimen is A. m. macrodactylum or the western long-toed salamander (as diagnosed by its unbroken dorsal stripe with blotchy patterns). Ambystomatids have a tendancy to hybridization. Ambistomatidae, like most derived salamanders, have an advanced tongue projection mechanism in which they literally squeeze tongue skeletal elements with muscles to shoot them forward for fast action.

Take a look at their clade here: The Macro Library.

Other weekly snippets:


  • Western Reptiles and Amphibians, Third Edition. Stebbins, RC, 2003.

Star Trek: The Review

Posted by tigerhawkvok on May 11, 2009 02:16 in General , sci-fi

So, I finally saw Star Trek. Time for a review!

--Warning: Gratuitous Spoilers--


Physics of Star Trek

Posted by tigerhawkvok on May 11, 2009 02:15 in General , physics , sci-fi

So, I'm sitting in the Berkeley BART, soon to head off to Pleasanton to go catch Star Trek with Jessica and some others (it occurs to me this is one of my few friends without a blog or site to link to!). Since I will have a lot of down time, and probably 3 hours of battery on my Eee PC, I decided I'd throw some "Physics of Star Trek" out there.

VOY: "Blink of an Eye"
Case: Time-Distorted Planet
Plausibility: Highly unlikely

While a nice episode with an interesting premise, the catch here that prevents it from entering the realm of plausible is the fact that time went faster for those on the planet, rather than Voyager. General Relativity provides for various forms of time dilation, including gravitational an other odd spacetime constructs that distort spacetime. However, all of these distortions increase your dilation, as "neutral" is flat, empty space. For your rate of passage though time to increase, your speed would have to be imaginary, so that when squared (IE, when calculating your spacetime interval along a Minkowski metric), you need to increase your rate of passage through time to be greater than unity (or c, depending on how you look at it).


Sketches ahoy

Posted by tigerhawkvok on May 08, 2009 20:20 in General

Plug for a friend! My friend Sara shares some webspace on my server, and for you readers, I wanted to direct you to some sketches she recently uploaded. Not shabby at all.

For the curious, the first picture is a Chamaeleo calyptratus, or the Veiled Chameleon. From chameleons, you get your word of the day: zygodactyly, which describes the arrangement of having toes pointing in opposite directions for grasping, much like parrots.

The frog drawing is just snazzy — I'm not sure which species it is.

It occurs to me, after entering this, that this would be a great Tuesday Tetrapod. Oh well.

Windows 7 So Far

Posted by tigerhawkvok on May 07, 2009 02:54 in computers

So far, I've fixed a video problem (needed ATI's Windows 7 update), audio problem, network problem (both needed reinstalled drivers), Hamachi problem (again, reinstall) ... I really want to like it, and I really like what works.

But, at least for the 64-bit upgrade path, there is something to not like:

Updates pending as things get fixed. In a bizzarre way, I hope it's my video card — then at least the problem will fix itself when it gets replaced ... if it's the 64-bit upgrade path, then HEY MICROSOFT. NEW BUG FOR YOU!

For those of you who run Windows 7 and want to send out a bug report, enter the following:

> rundll32.exe FeedbackTool.dll,ShowWizard

Now, can I fall asleep at 2am? That's the burning question.

UPDATE 1: Apparently, according to the TechNet forumns, this is a known (as yet unresolved) bug. Here's hoping they figure it out sooner rather than later.

Windows 7 RC Available

Posted by tigerhawkvok on May 05, 2009 20:43 in computers

For those readers who might want to test-run Windows 7 Release Candidate, I've uploaded a 7-zip package to http://filehost.revealedsingularity.net/Win7RC_Prep.7z that has:

  • A *.wmv video of how to install Windows 7 from a flash drive (via MS Taiwan, if I recall)
  • A text file with a link to the Windows 7 RC download
  • db.xml, a file to go with Microsoft's File Checksum Integrity Verifier utility. It contains the MD5 and SHA-1 hashes of the 64-bit RC.
  • The FCIV utility

You can download the release candidate over at Microsoft's site. I'd strongly recommend using a download manager, or a browser with one built in, such as Opera.

Once downloaded, you can display the hashes (MD5 and SHA-1) in the DB file, then compare them to your own. To do so, type at your command line:

> fciv -xml db_new.xml -sha1 7100.0.090421-1700_x64fre_client_en-us_retail_ultimate-grc1culxfrer_en_dvd.iso
> fciv -list -sha1 -xml db.xml
> fciv -list -sha1 -xml db_new.xml

If the two SHA-1 hashes match, your download is uncorrupted. Have fun! I plan on installing it myself in the next week or so. If someone bothers to hash out the 32 bit, let me know and I'll update this post with those hashes.

64-Bit hashes

  • SHA1: FC867FE1AB2E0A9796F9E4D155B44EA6998F4874
  • MD5: 98341AF35655137966E382C4FEAA282D

And just so it's not entirely worthless for everyone that is not interested, here's a background from Windows 7 Beta 1 (click for full size):

Daily Show and the LHC

Posted by tigerhawkvok on May 05, 2009 13:58 in physics , news , anti-science

The Daily Show has a brilliant segment on the LHC, and simply blasts the "OMGZ IT'LL DESTROY THE WORLD!" folk. Starts at about 8:57, but it should auto-play from there.

For my own take on this nonsense, see the post about the LHC.

Tuesday Tetrapod: Gavialis gangeticus

Posted by tigerhawkvok on May 04, 2009 22:00 in tuesday tetrapod

Another Tuesday Tetrapod! Today we have Gavialis gangeticus, or the Gharial, the most fully aquatic form of extant crocodylian.


G. gangeticus at the Honolulu Zoo, Hawai'i

One of only 23 extant species of Crocodylomorpha, Gavialis shares a clade with Tomistoma, of which specifics of their relationship are still contested. Reaching lengths of up to 6.5m, their dentition is adapted to a piscivorous diet. Gavialis has a home range along the Indian border, whereas Tomistoma is further south. Fossils of this clade date back to the Eocene. They are currently critically endangered.


  • Pough et al. 2004. Herpetology, 3rd edition.
  • Benton 2005. Vertebrate Paleontology, 3rd edition.
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