Friday, December 30, 2011

Winter break links II

"Texts From Cephalopods" -- in which all famous internet octopus videos are the same octopus, and it has an iPhone.

Flavor Network and the Principles of Food Pairing in new journal Scientific Reports classifies foods by the number of similar compounds they share and investigates whether different cultures pair like- or unlike-tasting foods more frequently.

Science quilts! (The biological ones are the most beautiful, of course, though CERN bubble chamber traces are nice as always.)

Friday, December 16, 2011

Winter break links I

Who's the Scientist?: Seventh graders describe scientists before and after a visit to Fermilab

Adorable tardigrade song

ANTARCTICA

“G-495, G-495, Gordon Valley. This is 3-6-Juliet inbound. You guys ready for us?”

We were not. And we knew they were inbound well before they called because we could hear the rotors echoing to us from down-glacier. It had been about 50 minutes since one of the National Science Foundation helicopters, call sign 3-6-Juliet, had dropped off Adam, Roger, and myself at our soon-to-be campsite for the next week. We were in Gordon Valley in the Transantarctic Mountains, a Middle Triassic (245 Ma) fossil site that had been fruitful in the past for both vertebrates and paleobotanical work (in the form of a standing petrified forest). In those 50 minutes we had to find an appropriate campsite, one that was on relatively level ground and offered us some sort of protection from the ferocious winds that could gust off the polar ice cap toward the frozen Ross Sea. The site we found was a few hundred yards from the helo site across mostly flat, but very boulder-ful, terrain. The goal was to get the supplies that had been dropped off at the helo site with us on the first run (cots, luggage, equipment, one of our diamond-blade rock saws (HEAVY), and a lot of food) to the campsite before the helo returned with the tent itself. Helicopter time is a precious commodity among research teams in Antarctica and we didn’t want to have to waste ours by making 3-6-Juliet hover while we finished. We did end up clearing the helo area after some quick and heroic heaving. As 3-6-Juliet descended I pulled the hood of my ‘big red’ Antarctic Program coat over my face and hid behind the helo landing area marker, a long strip of fluorescent orange plastic on the end of a piece of bamboo wedged between two rocks.

Sidor graduate students Brandon Peecook and Adam Huttenlocker pose in front of some wind sculpted sandstones from the Middle Triassic in Gordon Valley, Transantarctic Mountains. Mt. Falla is in the background.

The three of us had a very successful week camped out at Gordon Valley. The flat expanse we were camped on was littered with fossils, white chunks and specks sticking out against the brownish-red sandstone. In our first afternoon of exploration we found a number of specimens and marked them with cairns, little piles of rocks. The team had done reconnaissance here before my arrival and so a few cairns already existed. With all of these piles it was easy to get disoriented.

The tent. Our home away from home for about a week. We were the only living vertebrates in any direction for 30+ miles.

The most exciting specimen we checked out was a strip of bone sticking out of the hillside a few meters below the plane of our tent. Roger had concluded it was part of a temnospondyl skull. Temnospondyls were mostly large, aquatic predators during the late Paleozoic and early Mesozoic and may in fact be the group that modern batrachians (frogs + salamanders) came from. Only very little bone was exposed, about six inches of what was inferred to be the right cheek. After more careful prodding we found the same region on the left side of the skull. This told us that the skull was potentially complete (!) and that it was almost certainly upside down.

“Is it weird to only have the skull, with, like, no lower jaw or other body parts?” No, and especially not in this case. The rock layer it was found in was a conglomerate, an amalgamation of differently sized bits of rock (clasts) cemented together with finer sediments. This was also a river setting. As this animal decomposed and fell apart, the river likely transported some of its body. Given all this abuse it is no wonder that only the most robust, heavily ossified regions (like the skull) stand a chance of preservation.

Adam and I spent the week on that hillside using chisels and rock saws to dig a roughly triangular trench around where we believed the skull to be. We never hit bone while digging the trenches and we began to worry that perhaps the snout of the animal wasn’t even there. On the fourth day we decided to chip off the area where we thought we’d find the end of the snout… and there was nothing. This was disappointing, as we’d spent many hours preparing for a snout! As we moved in closer to where we knew there was bone, a big (non-fixable) crack ran through the now most snout-ward region of the block. When we pried the rock apart via this crack we were elated.

We could see many little teeth pointing up to the sky in praise! What’s more the crack had run right in front of the end of the snout, meaning next to no bone was lost. Huzzah! The skull ended up being about 32 inches long from braincase to snout-tip and is much narrower than more familiar temnospondyl skulls.


Adam and Brandon pose as the missing body of the 32-inch-long temnospondyl skull. The total body length would have been approximately 10 feet.

After three solid days of excavating, the rock-encrusted skull was wrapped with several rolls of duct tape, and on day 4 was lifted to the helicopter landing site to be transported back to camp (along with the rest of the fossils). The final weight of the block was about 200 pounds. The fossil is being prepped at the Burke Museum where it (and other Antarctic fossils) will ultimately go on display.

There are already two distinct genera of temnospondyl known from Gordon Valley, Kryostega collinsoni and Parotosuchus sp., and it looks like we may add a third. At this point anywhere else in the world paleontologists would use plaster to protect the fossil before removing it from the ground. In Antarctica, plaster = frozen powder, so we instead covered the skull with rags and wrapped it in duct tape. A lot of it. We used two 345-foot rolls going around and around the skull. Once the skull was free and fully wrapped Adam and I put it in the tent bag and, with the help of a shovel, carried all 200+ lbs. of it uphill to the helo area.


Parotosuchus sp., a temnospondyl discovered at Gordon Valley during a previous expedition.

Kannemeyeria, a large dicynodont therapsid. These large herbivores were incredibly common parts of terrestrial faunas throughout the Permo-Triassic. In South Africa they are the base of the Karoo's biostratigraphic system of correlating rock formations.

Cynognathus crateronotus. A large carnivorous cynodont therapsid that is a relatively close relative of the mammals. Antarctica was not a desert at the time.
Also recovered from Gordon Valley were limb elements and skull elements belonging to different therapsid (mammal-like reptiles, but never use this term) lineages, such as kannemeyeriid dicynodonts and the famous cynodont Cynognathus.

Many of these taxa are shared with the very well sampled Karoo Basin in South Africa. During the Permian and Triassic a number of basins formed along the southwest border of Pangaea in what are now Argentina, South Africa, Antarctica, and Australia. This is what got Christian Sidor, Adam's and my advisor, interested in Antarctic research in the first place. We know so much about South Africa and very little about other regions of southern Pangaea. Is South Africa truly representative? The largest extinction in the fossil record is at the boundary of the Permian and Triassic. We know a great deal about South Africa’s recovery. Is that how the world recovered, too?

Important lineages, such as basal dinosauromorphs, basal pseudosuchians (stem crocodilians), and many lines of aquatic reptile are known from similarly aged sediments from other parts of the world, but not South Africa. After our expedition we know that the basal pseudosuchians were in Antarctica at this time. By sampling more of the world we will get a better understanding of heterogeneity in global recovery. Also the Antarctic fossil faunas and floras are interesting in their own right for being at such high latitude. Though we know the poles of the planet were warm during the Triassic, plants and animals there would still have to deal with many weeks a year of constant darkness. How did they do it?

Adam and I are attending a NSF workshop next summer to discuss interests from different disciplines in another field camp in the Transantarctic Mountains. We’d like to go farther down range and sample some localities that are even lower in the Triassic, closer to the extinction boundary than Gordon Valley. Wish us luck!

Text by Brandon
Skull and "body" photos and captions by Adam

Wednesday, December 14, 2011

Nancy Schoeppner & the Ecology of Awesomeness

Originally posted at Rah Rah Radula.

I sure don't know Nancy Schoeppner at all.  She really flies under the internet radar, this is literally the only actual information I could find on her. I only paper-know her, as in I've read a handful of what I'm guessing is her PhD research with Rick Relyea at the University of Pittsburgh. But, in addition to being an EXCELLENT science communicator (I totally heart reading her papers!) and experimental biologist, her work has really shaped some of my, hitherto undescribed, thinking about how prey decide whether or not to be terrified.  There are various names for this sub-discipline of Ecology: Risk-Assessment, Inducible Defenses, the Ecology of Fear (Mwahhahahahaha! ...).

The quick and dirty is this: Hark back unto my first blog post where I described the terror of being an oyster and knowing a predatory snail was coming for you, grinding a hole into your shell, hell-bent on suckingyourgutsout! In that moment, that oyster can't really do anything about the snail, except hope he gets distracted by a pretty lady snail on an adjacent oyster and forgets about his hunger on his libidinous quest to pass his genes on (somewhat like terrestrial snails). But some organisms can tell when they're in danger and do something about it - even plants, I kid you not! Certain organisms can grow helmets and put spikes on their necks to make it harder for predators to eat them (so goth!), they can try to grow faster so that they get too big to be eaten by predators, or, well, they can run away and hide. These are called inducible defenses. Trying to figure out how these guys tell when they're in danger is, it turns out, really fun [for Emily].

Nancy's work has tested a bunch of hypotheses about risk assessment, and I think they are applicable to human decision-making in times of potential threat by carnivorous preadators (i.e., zombies, flesh-eating bacteria, Orca: the Killer Whale, etc.). So here are Nancy Schoeppner's:

3 Risk-Assessment Rules to Live and Die By

1. If you can smell your family being eaten, there's a pretty good chance you also are in danger of being eaten, and you should do something about it.

If you can smell your friends being eaten, there's still a good chance you're in danger, but maybe don't freak out so much. If all you can smell is some folks you don't even really know and have never met and who have a totally different diet and culture from you getting eaten - no biggie! It's not really your problem, becuase those other prey (suckers!) are so unlike you, the predator probably doesn't even recognize you as potential food! (NB: It's possible that this rule also guides US cultural attitudes and policy decisions.)

2. If there is a large cost to defending yourself, you should def. wait until you have good information that there is a serious, serious risk.

Tadpoles in Schoeppner's experiments only changed their growth patterns (very pricey, energetically, and also non-reversible, so they're screwed with their permanent giant tails if they're wrong!) when they smelled predators consuming AND digesting friends/family, but they changed their behavior (who cares?! You can just come out from your hiding space when you realize your friends were punking you, and all you lose is your dignity!) in response to less threatening smells.

3. Do the math, dummy.

If there's only one shark in the water (Fig. 1) but 500 tasty fat people, simmer down! Probably that shark will rip off somebody else's leg (phew!) and then realize humans taste like diet soda and a bitterness that can only be acquired from a lifetime of regrets. If the shark attacks randomly, the probability you will lose your leg is 1 in 500. But if you all panic, you miss valuable wave time, and increase the probability that you will get crushed by the 499 panicking morons on their way to shore. If, however, there are 499 sharks, and 500 people, the probability that you will leave the beach with all 4 limbs is 1 in 500, and so taking the chance of getting stampeded by your fellow prey is probably still a safe bet.


Fig. 1. Do not run from this shark - it probably won't rip your
leg off because, no offense meant, but it would probably rather
eat a brownie sundae. I put this picture in here because this post
is long and boring.

There are most certainly more rules, but these are the best supported. I hope to add my own rules some day. For instance, if you're on vacation, how can you tell whether that Italian man is ogling you because he's hungry, or because he likes the cut of your minigonna? Are there threat-signals that transcend international boundaries?

My point is that plants and animals seem to be very good at telling when they are safe and when they should hit the deck, and can optimize these situations to make sure that they will live long enough to make many, many babies. Even cooler, they do this all without actuarial tables, the Central Intelligence Agency, night-vision goggles (well some of them do have pretty good night vision), or even very sophistocated sensory systems. I have really benefited from Nancy's clear thinking and writing, and her thorough experimental technique - Swoon. I'd love to write a review paper with her some day - but these are merely the silly daydreams of a graduate student putting off other work...

Nancy Schoeppner - Selected Publications (in no detectable order):
1. Schoeppner & Relyea (2008) Oecologia. Detecting small environmental differences: risk-response curves for predator-induced behavior and morphology. 154:743-754.
2. Schoeppner & Relyea (2009) Functional Ecology. Interpreting the smells of predation: how alarm cues and kairomones induce different prey defences. 23: 1114-1121.
3. Schoeppner & Relyea (2009) Copeia. When Should Prey Respond to Consumed Heterospecifics? Testing Hypotheses of Perceived Risk. 1: 190-194
4. Schoeppner & Relyea (2005) Ecology Letters. Damage, digestion, and defence: the roles of alarm cues and kairomones for inducing prey defences. 8:505-512.

- Emily Grason

Monday, December 12, 2011

Mantis shrimp setae

Seen here is a photograph of the mantis shrimp (stomatopod) Odontodactylus scyllarus, a predatory tropical marine crustacean. The two oval-shaped "Dumbo ear" structures attached to its head are called antennal scales. They are composed of a flat lamina of cuticle surrounded by a fringe of red setae (hair-like structures). Interestingly, if one zooms in on these hairs, they bear a remarkable resemblance to bird feathers. A single hair actually has tiny hairs branching off of it, and the secondary hairs bear their own set of accessory hairs! It is not clear what function these antennal scale setae may have, if they have a function at all. Besides possible mechano- and chemo-receptive roles, I would be interested in exploring their potential hydrodynamic roles during fast burst swimming in Odontodactylid stomatopods (manuscript in press, to be discussed soon).

Stomatopod photograph by Jens Peterson
http://en.wikipedia.org/wiki/File:Odontodactylus_scyllarus1.jpg


Micrographs by Eric Octavio Campos

Wednesday, December 7, 2011

Smith Island Sampling

Originally posted at Beach Happenings at Diamond Point, Sequim.
Smith Island is the small island beyond Protection Island off Whidbey. Smith and Minor Island are connected by a beach at low tide. Like Protection, Smith now has a marine reserve status protecting the DNR owned sub-tidelands. On Friday a group of seaweed scientists all went out to Smith Island to make a permanent collection of who and what are living there.
This was our third attempt to go, and the weather was finally kind to us!

Dr. David Duggins took us out on the R/V Centennial from Friday Harbor Labs. Dr. Tom Mumford set up a video camera to record the seaweeds living on the
bottom. Next we towed a dredge behind the boat while divers carefully collected seaweeds that were more fragile. This photo shows the basket full of seaweed being lifted into the sorting table. Once the seaweeds are on the table, everyone gathers around, sorts the algae and calls off species names. Voucher specimens for pressing and microscope identification are collected into buckets and returned to the labs.

Dr. Bob Waaland is shown in this photo sorting through the many foliose reds like Cryptopleura. One thing that is immediately notable from dredge samples is that the algae on the bottom is mainly red! The way the light penetrates down to through the water and attenuates away red and yellow wavelengths favors pigments that can capture energy in the blue and green spectrum. - Megan Black

Sunday, December 4, 2011

Weekend links

Shrines to science. Does everyone have these, or mostly just those who do PCR?

The Bill Nye Effect is a grad-written blog covering a variety of disciplines including biograds. The sponsoring class is Science Writing for Impact from the program on the environment, and our own Emily Grason currently has top billing.

If you've ever made or used a computational phylogenetic tree, early bioinformaticist Margaret Dayhoff is someone you should know about.

Saturday, December 3, 2011

Happy GSS day!

Sorry for not posting yesterday -- there was a combination of a great Graduate Student Symposium, other obligations, and Blogger problems. All of you GSS presenters are in an excellent position to write blog posts now!

My vote for best phrase of GSS: "rugosity index." What was your favorite talk and why?