Saturday, May 31, 2008

We're baaaaack

and we will not be denied...

Friday, May 30, 2008

Weekly Urchin - what's in a name?

Chris at Echinoblog, coupled with the National Spelling Bee, gave me the inspiration for this week's urchin post.

Now, if you haven't heard, the green sea urchin, Strongylocentrotus droebachiensis, is my favorite urchin (yes, that's right, I said favorite urchin). But what, exactly, is the meaning of that name (certainly one of the longest species names out there)? This info was not easy to find, but with a little digging, this is what I've come up with:

First the classification:
Phylum Echinodermata
Class Echinoidea
Order Echinoida
Family Strongylocentrotidae
Genus Strongylocentrotus
Species droebachiensis

Now the various etymological roots:

echino - this was actually trickier than I thought it would be - from what I can tell the Greek ekinos means either 'hedgehog', 'sea urchin', and/or 'spiny'.

derma is Greek for 'skin'.

For Echinodermata, 'spiny skin' is the translation usually given, which makes sense. I like 'hedgehog skin' myself. Not so sure about 'sea urchin skin' to describe a group that contains the sea urchins.

Strongylo: from the Greek strogkylos meaning 'round'

centrotus: from the Greek kentrotos meaning 'spiked' (perhaps especially in reference to a type of spiked buckler)

droebachiensis: refers to Drobak, Norway where the species was first described

I guess this means that a literal translation would be something like 'spiky, round thing from Drobak'. Northern green sea urchin sounds better.

Wednesday, May 28, 2008

Serrefine, S-E-R-R-E-F-I-N-E, serrefine.

It's time once more for that weirdly fascinating event known as the National Spelling Bee (airs tomorrow and Friday). The kids are awkward (some more than others), yet there is something captivating about watching these middle school boys and girls triumph on national t.v., unashamed of their nerdliness. If you've never seen this event before, I highly recommend catching some of it - Tivo the finals if you can - I'm willing to bet you won't be able to click away from it.

Friday, May 23, 2008

Friday Dial Stopper: the Sunlight Zone edition

I must thank Miriam over at The Oyster's Garter for this week's dial stopper - she posted this Dresden Doll's video and I thought it was simply brilliant the moment I saw it. So I stole it.

Does that video look familiar? It should (and therein lies its brilliance):

Wednesday, May 21, 2008

Critter collecting

I just came across this blog that documents a fish critter collecting expedition in the Bahamas by the President of the New England Aquarium. The collecting has finished (and thus the blog as well), but this "behind-the-scenes" account of the week-long trip is an interesting read.

Tuesday, May 20, 2008

Dr. Ian Malcolm would not like this

Forgive my Malcolm-esque skepticism, but this "solution" to Australia's cane toad problem sounds like a bad idea:

Native animals, such as quolls, goannas, snakes and crocodiles, that eat the toads usually suffer an agonising death. The bigger the toad, the greater the dose of its poison, and the greater the chance the predator will die.

Lab work by Rick Shine at Sydney University and his team shows, though, that if an animal eats a small cane toad and manages to survive, it doesn't usually repeat the mistake. "It's astonishing how quickly fish, frogs and some small mammals are learning to avoid the toads after a bad experience," Shine says.

He now proposes taking advantage of this by releasing baby, sterile male "teacher toads", in advance of the invasion front. Native animals that ate these small toads would probably vomit up their meal, but survive – and should then steer clear of the larger, deadlier toads when they arrive....For good measure, he says, the teacher toads could also be infected with a lung worm parasite that targets only the toads so that they won't start invading themselves.

Clearly, I am no expert here, but what percentage of intentionally released non-native species has worked out as expected? Why do I get a feeling that ten years from now we'll be reading about Australia's native amphibians succumbing to an invasive lung worm parasite, yet "surprisingly" the cane toads will still be around and poisoning the native wildlife?

Perhaps this is just my knee-jerk bias against introducing non-natives to an area rearing its ugly head - as one commenter suggested when I wrote about Pleistocene rewilding - but I don't see how adding more cane toads to the picture is a sustainable solution.

As reported in New Scientist

Friday, May 16, 2008

Friday Dial Stopper - Cookie Monster Edition?

This week's dial stopper brought to you by one of the best live bands in the history of music. And the letter 'C'. (confused? you must have missed this post)

And if you need a refresher on what Cookie Monster sounds like:

Thursday, May 15, 2008

Weekly Urchin: Crash and Burn Edition

Click on image to enlarge
Data from the National Marine Fisheries Service

How's this for a poster child of overfishing and mismanagement? (actually, to be fair, I imagine that the sudden rise in urchin demand in 1987 took the fisheries folks by surprise and by the time they implemented a management plan, it was already too late.)

Can somebody explain this to me?

(no, this isn't a picture of Jack)
Remember that stack of papers I have to grade? Well, I'm still working on them. But I had to stop and vent some frustration. Tell me how I interpret this:

One, single project, with four group members, on the effect of two different diets (Artemia and copepods) on jellyfish growth and budding. Here are summaries of each student's account of their methodology:

Student 1 - project ran for 23 days, fed jellyfish 10ml of the two different diets at first, then reduced to 5ml after 10ml was deemed too much.

Student 2 - project ran for 4 weeks, fed jellyfish 1ml of both diets.

Student 3 - project ran for 6 weeks, fed jellyfish 3ml of both diets.

Student 4 - project ran for 4 weeks, fed jellyfish 1ml of one diet, 5ml of the second

It's one thing (and expected) for members of a team to differ in how well they explain their experimental procedure - some leave things out that others include, some are more concise and understandable, but no one in this group agrees on the day-to-day details of the experiment. How does that happen?

Does this mean they didn't actually do the experiment and made stuff up? Was this a complete breakdown of teamwork and each individual did their own thing? Did one student do the whole thing and then screw with the other three by telling each something different?

Tangled Bank #105

The Tangled BankThe Beagle Project is the latest host for The Tangled Bank - a great collection of biology-laden posts.

While you're there buy a t-shirt or make a donation to their project!

Wednesday, May 14, 2008

Dicky B and Cookie

In the car this morning a song by the Mighty Mighty Bosstones came on the radio. My daughter was fascinated by the lead singer (Dickey Barret). First she commented that his voice sounded strange. Then, after listening for a while she came to the conclusion that he sounds just like Cookie Monster. As I listened more closely myself, I think she might be on to something.

(for those of you unfamiliar with the Bosstones, I'll have something up on Friday to help make the Cookie Monster connection)

Sunday, May 11, 2008

Ebb & Flow

Would have been better if had a tripod. Next time.

Saturday, May 10, 2008

Quick hits

The platypus genome put me in the mood for more evolutionary biology, so here are some interesting recent papers of an evolutionary bend (note: Abstracts available, but subscription or "pay-per-view" needed for full article access. Sorry.):

Amino acid sequence data from collagen extracted from the bones of Tyrannasaurus rex and the mammoth, Mammut americanum, were used to build a phylogeny of these two species. As expected, based on previous phylogenetic work, M. americanum groups with modern elephants and T. rex groups with modern birds (chickens to be exact). This paper builds on earlier success in using protein sequences to elucidate evolutionary history of extinct organisms.

Hermaphoditism evolves when mate-search efficiency is poor. In other words, if ... you ... move ... really ... slowly ... and ... don't come across another individual of your species all that often, it's best to be prepared when you do - it would really suck to look all that time for a mate only to come across an individual of the same sex and have to start the search all over again.

Analysis of oxygen isotope levels in the tooth enamel of extinct relatives of elephants suggest that modern probocidians evolved from aquatic or semi-aquatic forms. This is expected given the close phylogentic relationship between extant elephants and the sirenians (manatees and dugongs) and provides new arguments for the idea that elephant trunks may have originally evolved as a snorkel.

Wednesday, May 07, 2008

Weird animal, not-so-weird genome

(After reading PZ Myers's post on the matter, I've decided to stop using "weird" to describe the platypus's genome. However, I still think the animal itself can aptly be described as weird.)

Nature reports today that the platypus genome has been sequenced by a large international team (note: subscription needed for full article). Fittingly, it seems that the genome is just as delightfully weird interesting as the platypus itself - a mixture of mammal genes interspersed with ancestral reptilian and avian sequences, with a bit of novelty thrown in, all of which tells us a great deal about mammalian evolutionary history.

Some highlights:

  • The sequenced genome, with all of its peculiarities details, corroborates the idea that the platypus lineage is the earliest diverging mammalian lineage - diverging from the rest of the mammals over 160 million years ago. Side note: the marsupial-placental split occurred ~150 mya, and all modern placentals orders appeared by ~75 mya.

  • The genes for caseins, the proteins found in milk, align well with the casein gene families found in other mammals. This suggests, as expected, that milk production evolved before mammals evolved live birthing (or nipples - platypus secrete milk through pores in the skin).

  • Speaking of birthing, the platypus genome contains sequences that match mammalian genes for the zona pellucida, but also has copies of zona pellucida genes previously only found in amphibians, birds and fish. There is also a gene for the yolk-stored proteins, vitellogenins, that are also found in amphibians, reptiles, and birds, but that have been lost in non-monotreme mammals.

  • Genes for the proteins found in the platypus' reptilian-like toxins turn out to be novel sequences, independently evolved and are not homologous with reptile toxin genes. Toxin production in reptiles and platypus seems to be a case of convergent evolution. Interestingly though, the same defensin genes were co-opted in each case.

  • (Note: I was going to strike the word weird from this item, but I've decided that this is indeed weird.) Weirdest of all might be the sex chromosomes. Platypus sex chromosomes are known to be strange structures cytologically speaking, but it turns out that none of their X chromosomes match the X chromosomes of other mammals - they're more like the Z chromosome found in birds. A "normal" autosomal chromosome however matches the mouse X chromosome.

  • microRNA sequences are all over the place - platypus have both microRNA sequences that are found in birds, but not mammals, as well as microRNA sequences that are found in mammals, but not birds.

    Further study of the genome will certainly add to the uniqueness of the platypus and will be helpful in understanding early mammal evolution. I think it's rather poetic that such an odd cool creature has such an odd cool genome. Wouldn't it have been disappointing if it didn't?

  • Tuesday, May 06, 2008

    Circus of the Spineless

    Kevin Zelnio has the latest edition of the Circus of the Spineless up at Deep Sea News. Go check it out.

    It's that time of year again...

    By the end of the day today, I should have a stack of papers to grade. Woohoo!! My intro bio students undertook a "semester-long"* research project and their formal write-ups are due today. What are the chances that I have them all before I leave? Yeah, that's what I think too.

    The students gave group presentations of their research last week, so I have a good feel for what to expect. I've flipped through some already and have found that my oh-so wonderful suggestions I gave after their presentation have not been incorporated into their final paper. Not a good start. But at least some of the students stopped referring to earthworms as insects. So they've got that going for them.

    *Apparently, "semester-long", for some groups, means wait until the last weekend before everything is due to collect and analyze samples and then when they realize they don't have enough time to actually quantify anything, they "eye-ball" it.

    Friday, May 02, 2008

    Weekly urchin - new toy edition

    Part of my job as coordinator of the Undergraduate Center for Marine Life Sciences is to purchase equipment that could be used by students and faculty for research. The newest edition to the Center is a Sea & Sea DX-1G digital underwater camera and strobe. It seems on first inspection to be a marvelous piece of equipment. (Thanks, Rick, for using your power and influence to coerce some useful camera feedback from your "peeps" for me)

    The second the battery finished charging, I grabbed the camera and headed down to the RWU wetlab to try it out. I must say that I'm really impressed with the quality of the images this camera takes, especially since these test shots were taken with me just sticking the camera into a bunch of tanks, hoping I was focusing on something, and using only the built-in flash instead of the big strobe. With some fine-tuning I think this will take some phenomenal shots out in the field.

    First up, Strongylocentrotus droebachiensis, of course:

    Here's an oyster toadfish trying to hide:

    Apparently tautog like to snuggle with toadfish:

    Lined seahorse:

    Fire shrimp:

    Baby Juvenile jawfish:

    The clownfish thought I was going to feed them:

    Thursday, May 01, 2008

    Probably doesn't taste like chicken

    Drop what you're doing and go check out Coral Week at Deep Sea News - everything you never wanted to know about those cnidarious crusteose critters.

    Better yet, start with ChrisM's post about echinoderms that eat corals.