Chytrid fungus in plethodontid salamanders

Posted by tigerhawkvok on December 18, 2009 16:47 in General , biology , research , misc science , herpetology

Yes, I know I failed on the Tuesday Tet. I know what it will be (and will be a double-feature next week), but I couldn't bring myself to do a short entry without some research first.

Also, the entry on the basal theropod (DOI 10.1126/science.1180350) will be coming. More importantly though, I wanted to note that my good friend Sara Weinstein had her first paper published in Copeia today. You can view the abstract at asihcopeiaonline.org ("An Aquatic Disease on a Terrestrial Salamander: Individual and Population Level Effects of the Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis, on Batrachoseps attenuatus (Plethodontidae)" DOI: 10.1643/CH-08-180). I'll post a nice summary of it in an few days, also. Hopefully that will be somewhat illuminating, as I've known about this project (and helped a little bit) for 3-4 years now!

Now, I just need to get myself in gear and get *my* paper out. 9 months is just embarassing.

Randall Munroe does it again

Posted by tigerhawkvok on December 13, 2009 23:08 in General , anti-science

Really says it all.

Basal theropod, with interesting implications

Posted by tigerhawkvok on December 10, 2009 15:35 in dinosaurs , evolution , paleontology

Now, this is actually an interesting piece. according to LiveScience, a new basal theropod dinosaur, Tawa hallae has been found in lower Triassic New Mexico rocks, dated at ~213 MYA. The paper is due to be published in the December 11th issue of Science, after which I'll post more.

However, LiveScience implies that there is reason to believe that T. hallae was covered in filamentary integumentary structures, adding to the evidence suggesting filamentary integument was at least basal to dinosauria (interesting blog post on that topic, though this find, if LiveScience's implications are correct, would invalidate his point (5).)

To avoid needless speculation, though, I'll avoid talking more about it right now, and instead post a longer entry on it in the next few days when I can look at the actual paper. But I'm looking forward to it!

You, Data, and the Internet

Posted by tigerhawkvok on December 10, 2009 12:25 in General , computers , internet

This says it all:

A Day in the Internet

Created by Online Education

Tuesday Tetrapod: Atelopus zeteki

Posted by tigerhawkvok on December 09, 2009 02:49 in tuesday tetrapod

Another Tuesday! And I've noticed a horrible fact: I've so far neglected an entire, speciose, clade! To work on remedying the situation, I present Atelopus zeteki, or the Panamanian Golden Frog.

A. zeteki by Flickr user brian.gratwicke

Part of the horribly polytomacious (is that a word? Of many polytomies?) bufonid family in the neobatrachian clade, A. zeteki is probably extinct in the wild. They communicate by visual signals, such as 'hand waving', rather than primarily vocally.

A. zeteki is almost certainly extinct in the wild, and remains only in isolated populations maintained in captivity. Their populations were decimated by the chytrid fungus affecting frogs and salamanders, and numbers were further supressed by poaching. As such, they are IUCN critically endangered.

You can also see more about them in Attenbourough's Life in Cold Blood.

Emacs, ruler of the world

Posted by tigerhawkvok on December 08, 2009 19:13 in programming

Ignore this for the moment. This is just a test post using Emacs and XML-RPC to post to the blog.

Seems that this may not work with categories. Hm.

Perils of Non-FOSS

Posted by tigerhawkvok on December 08, 2009 18:41 in research , programming

Poking around my archives, I find that I've somehow managed to lose my IDL installation backups, while keeping my carefully configured startups and such. Of course.

Seeing as I had a bout of inspiration to do work on my research and, well, finally re-submit it (It's been nine months!), I suddenly find that my customized scripts to churn out quick calculations and the nice eps plots are useless, as I can run IDL for all of 15 minutes.

Damn. I need to see what Python's plotting options look like. Look for a tetrapod post later tonight.

Atheism, Protheism, Theism, and Debate

Posted by tigerhawkvok on December 07, 2009 21:22 in General , religion

So, today when hitting up the blogs (in-between bouts of productivity), I ran across this post on SkepChick (amusing fact: guys write for skepchick too).

The nuts-and-bolts:

Honestly, I'm extremely bored with the god/no god debate. I don't care. Really, I don't care. Believe whatever you want about god(s)(ess)(es). It doesn't matter. Sure, I think it's all a bit silly, and I don't buy into it, but I know plenty of really smart people who do. And I know a few really smart skeptics who do... a couple who are even *gasp* Christians!

Unless you're using your religion to spread evil -- like killing your daughter for talking to the guy you didn't choose as her husband or trying to pass blatantly bigoted laws denying groups of people their basic rights, or trying to teach my kid that dinosaurs were here just a few thousand years ago and that The Flintstones are based on a true story -- really, just thinking that there might be a deity isn't an intellectual crime in my mind.

Religion isn't above scrutiny, but I don't think it's necessary to mock the religious and spew hatred at them for merely believing.

Michael Shermer just wrote a whiny article on not beating up the believers, but I really loved Brian Thompson's article over at Amateur Scientist, and highly recommend you read it after answering today's quest

What's your take on the atheists vs religious "war"? Do you think we should be more tolerant? Do you think we should be less tolerant? Does it matter?

The Afternoon Inquisition (or AI) is a question posed to you, the Skepchick community. Look for it to appear daily at 3pm ET.

While in principle I agree, I feel that factually this is not a tenable position. The fact of the matter is that religion influences politicians, and thus directly impacts everyone's life. Whether you're atheist, pagan, wicca, asgardian, jewish — what have you — you have the right to not by tyrranized into the view of a Christian majority. If the majority was any other religion, then the minorities would still retain the right to avoid tyranny by the majority. It is insane that religious viewpoints can dictate rights in any manner. Pick your favorite debate here.

I'll even define a term: "protheists". This is an evangelical theist, someone that beyond mere "belief", tries to assert that belief onto others by evangelism, policy, etc.

The fact of the matter is that atheists (and, for that matter, theists) should speak out against religion in the public sphere. After all, think of last year's nativity scene in Washington. Would a theist prefer Zeus, FSM, and Isis represented alongside their nativity? Or skip out on it altogether?

It's a simple matter of equality. And while religion pervades our government, it's unobtainable, virtually by definition. So we should continue to debate, loudly, against religious-induced ignorance. Here's a good benchmark: see when there's not a frenzy in the media when a president *doesn't* mention their deity-of-choice (ie, the Abrahamic god). Till that day happens, there's too much religion in our politics.

However, casual faith? People who may or may not go to church/synagogue/what have you? Eh. That's generally not harmful. I think it's counterproductive, and bothers me from an efficiency standpoint, but I know plenty of people like that and I give it a resounding "meh". It's about as relevant as people who hunt-and-peck with single fingers staring at a keyboard. A pretty glaring waste of time in my opinion, but doesn't hurt anyone. (In my opinion, it's already a weak form of atheism with cultural overtones, but that's a different post).

So-Called Climategate

Posted by tigerhawkvok on December 06, 2009 21:37 in anti-science , misc science , public science

Note: This references file version "d", which seems to be the one generally discussed. There is a later version, "e", that never made it into any used/published data sets.

Oh, "climategate". How you are poorly reported.

It recently came to my attention that, awesomely, much of this OMGZ CODE OF EVIL was written in IDL. Now, having done astronomy research in IDL, all my undergraduate data reduction in IDL, and my (horribly behind) sauropod research in IDL, I feel like I can competently comment on the code here.

So, this artificial decline hiding? Well, we can take a look at ./FOIA/documents/osborn-tree6/briffa_sep98_d.pro (aside: if you want to see the leaked data yourself, being aware that the data was illegally obtained, you can download it via BitTorrent and this magnet link: magnet link). They say a picture is worth a thousand words, so, let's start with a picture:

source in Emacs 23.1.1 buffer

Printscreen of emacs. The whole code, in all it's beauty. Click for a full-sized version.


Darwin Christmas, and Finding Control Groups

Posted by tigerhawkvok on December 06, 2009 19:18 in evolution , biology , misc science

I find this incredibly entertaining:

Darwin Christmas

"Darwin Christmas". Hotlinked since it lives on Imageshack.

Arguably the greatest problem with it is that we're programmed from a young age to think of left-to-right as increasing on a given axis, though obviously this is meant to be read from right-to-left.

In other news, this "weird science" post from Ars Technica comes with this entertaining gem:

This is little more than a press release on some research in progress. Still, even before the results are in, the process of setting up the experiment turned out to be rather informative. The study, you see, is on porn consumption, and it looks like the researchers will be stuck working without anybody to act as a negative control. "We started our research seeking men in their twenties who had never consumed pornography," said Simon Louis Lajeunesse. "We couldn't find any."

Time to stop procrastinating and start properly bolting out those grad school applications.

Zooseum Redux

Posted by tigerhawkvok on December 04, 2009 18:31 in General , biology , misc science , public science

I realized that the Zooseum has the flaw that on wet, cold, days, neither aspect of the zooseum would attract customers. However, this problem is easily rectified by having an underground portion of the zooseum.

Located centrally under the zooseum, you can locate the food court and a few stores (with, of course, others by the entrance/exit). Throw in some paths with moving walkways to connect exhibit to exhibit, and arial enclosed connections for nearby exhibits (think Birge-LeConte, or parking structure-airport in L4D's "Dead Air").

This provides an all-weather aspect to the attraction, and means that unlike most zoos, the hours of operation don't need to be strictly confined to animal activity. With hidden paths, lighting does not need to account for disturbance to the animals, as the interconnects can be well-lit, but being underground, should provide little to no animal irritation. Though animal activity will drop off, all that becomes needed are suggestions or notices that there will be reduced animal activity after a certain time can be made, and with longer operating hours, the zooseum should see a higher profit than a standard zoo *or* museum.

Broadly acceptable public option?

Posted by tigerhawkvok on December 04, 2009 04:05 in politics , medicine

Just a quick post ... but here's a thought on the public option.

It's been brought up that the real trick to getting healthcare reform through the senate is to have a public option weak enough to attract swing votes but strong enough to not repel strong votes. I think this construction would do it:

  • All states have a weak public option they can opt out of. It begins weaker than the initial senate proposal. Opt out can be done only by public vote with a majority. Opt-out can be pushed only once every five years.
  • If after one year, the relevant factors have an insufficient change (uninsurance rates, fraction of income, mean insurance prices, etc), this changes to the current House version of the public option. This is stronger and has a strong public rate negotiation. This is a "trigger" phase one. This phase is automatically triggered if states that "opted out" fail federal guidelines five years after bill passage.
  • Two years after this (so, three years after the bill takes effect), if set targets are not made, in that state public option rates change to strong medicare negotiation / single payer rates. This is a phase two "trigger".
  • So, it begins weak enough to appease conservatives (so, if weak public option/other measures are sufficient stronger versions will never take effect, combined with an opt-out mechanism). If this is insufficient (in my opinion, the likely case), it changes to a moderate level public option, and once again the market is given a time frame to stabilize (and thus, a chance for the measures to take effect). Evaluation after this period then reverts to a strong public option.

    Thus, every level of "belief" in the public option is given a fair shake, beginning with minimal-intervention, mostly market shaping and depending on the level of ineffectualism, it would reach a stable point within each state.

    I actually really think this is sellable to all all stripes of the political spectrum.


Posted by tigerhawkvok on December 03, 2009 00:05 in General , biology , misc science , public science

Zoos are awesome, and so are museums. So, I wonder, why has no one taken the obvious step and combined natural history museums and zoos?

I think the way you do this is that the physical layout of the "zooseum" echos a phylogenetic tree. Different branches are linked up by aerial cable cars, giving a nice set of sightlines while preserving the message of evolution and interrelatedness of animals. Along these branching paths, there are interspersed buildings with fossil representations and extinct members of lineages.


Sample layout. Red lines represent potential arial paths.

In addition to this being a largely natural layout for the animals and fossils on display, this also helps instill a proper phylogenetic way of thinking for visitors. Thus, aviaries would be most closely placed to crocodile and alligator enclosures, and between the two would be exhibits on non-avian dinosaurs and pterosaurs. Additionally, finally, Dimetrodon would be placed in fossil exhibits on the ways to the mammal section of the "zoo", and any oceangoing mammals (ie, dolphins or porpoises, with whales being obviously unfeasible) would be most adjacent to hippos, pigs, and cervids, and bovids.

Despite the "unusual" layouts mentioned in the last paragraph, much of the layouts are quite natural. The cats are together, birds of prey are together, snakes are together (and closest to varanids), etcetera. This also provides the unique opportunity to provide an insect/arthropod exhibit that presents relations of these generally underdescribed (both in the literature and in the public) animals.

This "zooseum", then, is effectively a one-stop shop for the natural world. The unique display mechanism and unique content could also provide a draw for personnel, and good merchandising opportunities. The purpose of the museum portions would be more education than research, with (therefore) few real fossils and mostly casts, emphasizing comparative biology and morphologies. The aerial paths connecting various groups could be centered around the amniote split, acting like a hub.

Perhaps this entry was kind of rambly, but I felt like this is a nifty idea, and I wanted to post it — any thoughts?

Tuesday Tetrapod: Opisthocomus hoazin

Posted by tigerhawkvok on December 01, 2009 22:37 in tuesday tetrapod

Reading Dawkins' Greatest Show on Earth has got me feeling the "groove" for ancestral relationships and the like, so today's Tuesday Tetrapod reflects that. I bring to you Opisthocomus hoazin, or the Hoatzin:


O. hoazin. Image CC-BY-NC by Flickr user codiferous.

The bird is endemic to northern South America, roughtly pheasant-sized. It has the dubious honor of being perhaps the worst phyletically resolved of extant aves.

Hoatzin chick

An image of a Hoatzin chick climbing by virtue of its claws. Sadly, this image comes from a protheist, history-denying site over here. That's a surprisingly hard image to find. Image is copyright the owner, and linked on their server.

O. hoazin is also interesting for a number of phylogenetic reasons. It's the only member of opisthocomiformes, part of the poorly-resolved area of avian phylogeny in neoaves. It also has the interesting adaptation of having three fully articulated digits, in an apparent atavism (reversion) to the basal deinonychosaurian form. These digits fuse in adults to the more standard neoavian condition. Needless to say, aside from an interesting fact, it's a wonderful peice of persuasive evidence of the archosaurian lineage of birds.

Emu manus claw

Image of an Dromaeus novaehollandiae's manual claw from Matt Wedel's Dr. Vector blog.

Primarily herbiverous, the Hoatzin performs fermentation in its crop, similar to the function of the rumen in ruminants. This means that the odors associated with fermentation are unusually ... available ... with O. hoazin, giving it the nickname of 'stinkbird'. The size of the crop displaces the flight muscles and reduces the keel, thus impacting the flight ability of these birds. Luckily for the birds, though, this is reputed to give the meat a poor taste, meaning they are rarely hunted (though occassionally tamed).

The hoatzin population is stable over a large area, and as of 2009 is rated IUCN least concern. Feels good to talk about an animal that isn't about to disappear for a change!

Wrongheaded Creationists 4: Hitler was an "Evolutionist" (Not)

Posted by tigerhawkvok on November 25, 2009 14:24 in evolution , religion , anti-science , creationists

This comes up so often, it needs a token response. Creationists (mostly) assert that Hitler was an atheist who used evolution to promote extermination of Jews. This is blatantly and verifiably incorrect.

First, so what? Even if he understood evolution and accepted it (he didn't), the fact he liked to drink beer doesn't make all beer-drinkers in favor of eugenics, anti-semetic, and dictatorial.

As to the point itself, here's a rebuttal, courtesy of Hitler himself, yanked from a comment over at Pharyngula:

In Mein Kampf, Hitler asserted the fixity of species, that god made man, that man existed "from the beginning" and did not descend from apes, that man was made in the image of god and was expelled from the garden of Eden, and that Jesus was his inspiration.
His words:

The fox remains always a fox, the goose remains a goose, and the tiger will retain the character of a tiger. - Adolf Hitler, Mein Kampf, vol. i, ch. xi

For it was by the Will of God that men were made of a certain bodily shape, were given their natures and their faculties. - Adolf Hitler, Mein Kampf, vol. ii, ch. x

From where do we get the right to believe, that from the very beginning Man was not what he is today? Looking at Nature tells us, that in the realm of plants and animals changes and developments happen. But nowhere inside a kind shows such a development as the breadth of the jump , as Man must supposedly have made, if he has developed from an ape-like state to what he is today. - Adolf Hitler, Hitler's Tabletalk

Whoever would dare to raise a profane hand against that highest image of God among His creatures would sin against the bountiful Creator of this marvel and would collaborate in the expulsion from Paradise. - Adolf Hitler, Mein Kampf, vol ii, ch. i

My feeling as a Christian points me to my Lord and Savior as a fighter. It points me to the man who once in loneliness, surrounded only by a few followers, recognized these Jews for what they were and summoned men to fight against them. - Adolf Hitler, speech, April 12 1922, published in My New Order

Hitler was a creo.

Yes, Hitler was a strong Christian and unabashed creationist. This does not equate creationists to Hitler, however. They're pretty foolhardy and willingly blinded all on their own accord, with no ties to Hitler's filth necessary.

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