Me and Terry Hughes, we got Kwan

This is a little spooky. Terry Hughes of the Center for Excellence in Coral Reef Studies in Australia, whom I know only vaguely, has been quoted on the topic of the Shen Neng 1, that Chinese coal ship that ran aground on the Great Barrier Reef. His somewhat dismissive tone sounds creepily like my recent rant on the subject.

He said:
"The [Shen Neng 1] ship grounding, in the scheme of things, is not a major incident. It's bad if you happen to be one of the corals the ship parked itself on, but it's tiny in the face of the real problem: global warming."

I said:
"I am not worried in the slightest about this incident.  Not that its a good thing - far from it - but this accident is nothing more than a tree, obscuring us from seeing one big and scary forest [burning fossil fuels]."

Terry, you're my Ambassador of Kwan.

Play Bit-o-critter, round 13

I need a scientific name.  Anyone?  Bueller? 

While we're talking genomes...

...here's something distinctly more marine. 

A little while ago I drew attention to Andrea Marshall's paper showing that there's not one but possibly three species of manta ray (see Whats A Manta Do?).  In the preamble for that post, I drew analogy between mantas and killer whales as monotypic species; that is, the only members of their genus, a taxonomic one-of-a-kind.  Well blow me down if some new genomics work with killer whales doesn't suggest that there's more than one species of those, too!  Morin and colleagues used a different approach than Marshall, whose work was mostly based on colors and patterns and tooth shape.  Instead, they used "massively parallel pyrosequencing" (try saying that with a mouth full of marbles) to show genetic differences in the mitochondrial genome.  So what the heck does that mean?  Well, lets just say its sequencing a whole bunch of DNA at once, using DNA not from the nucleus of the cell, but from its engine room: the mitochondrion.  The technology is actually a really, fantastic example of miniaturisation; perhaps I'll write about it one day.  But, I digress...  Morin and friends recommend three species of Orcinus orca, with two more subspecies as well.  Subspecies are not required by the taxonomic code, but they are eligible for separate protections under the Endangered Species Act, so its a meaningful result for conservation biologists too; they'll now have to make assessments of each species and subspecies to see which, if any, require additional protections.

To the experts, its not a total surprise that there are multiple species in either of these groups.  You can bet your bum that they set out to confirm a hunch that there are more than one, leaving the surprise for the rest of us less familiar with these beasties and who never saw the subtle differences.  That's OK, I like surprises, especially when they involve new and unexplored diversity, right under our noses.  Maybe we should take a harder look at a few more monotypics, for the inevitable species flocks hiding in the details or the DNA.  Whale sharks, basking sharks, Mola, anyone?

Morin, P., Archer, F., Foote, A., Vilstrup, J., Allen, E., Wade, P., Durban, J., Parsons, K., Pitman, R., Li, L., Bouffard, P., Abel Nielsen, S., Rasmussen, M., Willerslev, E., Gilbert, M., & Harkins, T. (2010). Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species Genome Research DOI: 10.1101/gr.102954.109

In which I concede that Sigourney Weaver is OK

I never really cared for Sigourney Weaver, despite the fact that she stars in several of my favourite movies - Alien/s, Ghostbusters & Avatar.  I don't know why, she always just seemed wooden to me (maybe I just don't recognise a stoic heroine when I see one).  Now, doubtless influenced by Cameron and his obsession with all things marine, she is going to Washington to advocate for urgent action regarding that other great impact of global warming: chest bursting aliens, giant ghost dog gargoyles of Gozer, ten foot blue people of Pandora, ocean acidifcation.

Good on ya 'Gourney, you're OK!

Complete genome from a single cell - well, yes, *technically*

Its not quite marine science (hey, its my blog, so nerrr), but there's a paper in PLoS One this week where the authors describe the assembly of a genome sequence (all the DNA from beginning to end) from a single cell of a bacterium.  Normally it would take a whole bunch of cultured cells to do this, which limits genome sequencing to those bacteria that can be cultured and right now that isn't many (probably less than 10%).

Having announced this great achievement (and it is) in their abstract, the authors go on to point out that this particular bacterium, a symbiont from the gut of an insect, is polyploid.  In other words, it has multiple copies of the whole genome per cell - in fact, up to 900 copies!  So, while its technically correct that they sequenced a genome based on a single cell, you'll forgive me for thinking they're gilding the lily a bit.

While we're at it, who is proofing manuscripts at PLoS One these days?  The last sentence of the abstract reads: "This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes."  Huh?

Woyke, T., Tighe, D., Mavromatis, K., Clum, A., Copeland, A., Schackwitz, W., Lapidus, A., Wu, D., McCutcheon, J., McDonald, B., Moran, N., Bristow, J., & Cheng, J. (2010). One Bacterial Cell, One Complete Genome PLoS ONE, 5 (4) DOI: 10.1371/journal.pone.0010314

XKCD gets me

If you guys don't subscribe to xkcd.com, you really should; the cartoons are simple, pithy and often extremely creative.  Not always laugh out loud funny, but neither was George Carlin, and he was a comedic genius.  I especially like this one; it captures that out-of-sight, out-of-mind thing that infects so many folks when it comes to the oceans.  Of course, now that I've analysed it, its lost all chance of being funny.  Especially with that post-script, bringing your attention to that  fact. And now that last sentence.  And that one.              and that one....

Play Bit-o-critter, round 12

This round is a 6-pack for the fish-heads among you.  Between the bits, you ought to be able to get the group.  Then I need species names for all six.

Critter A

Critter B

Critter C

Critter D

Critter E

Critter F

Solutions to bit-o-critter 9, 10 and 11

Hi all,

I got a bit behind while I was in NY, but am back on deck today and will be back to posting a bit more regularly.  Here's the solutions to the recent bit-o-critters.

Round 9 - Six-gilled shark, Hexanchus griseus
A big ol' slug of a shark, most common in the colder waters of the world.   I picked it because it always seemed odd to me that six and seven gilled sharks manage to have one or two more than everyone else.  Five seems kind of a fundamental number for gills.

Round 10 - Bobbit worm, Eunice aphroditois.  This is a large (like, 5 feet long) and scary polychaete or bristle worm.  It mostly hangs out in the pose shown, waiting for some unfortunate fish to swim past the jaws or brush the antennae, then BAM!  The ant lions of the worm world.  Nicknamed after, you guessed it, Lorena Bobbit (remember her? snip! snip!)

Round 11 - Loriciferan.  OK, that was just mean.  A truly obscure group of microscopic invertebrates that live between sand grains on the bottom of the ocean.  A phylum unto themselves, they were only discovered in 1983.  Not much to them except the lorica or house (the clear baggy bit on the right), some somatic and reproductive cells (pink) and the ring of tentacles around the oral cone (on the left).

Hints for bit-o-critter rounds 9, 10 and 11

I guess I got carried away with making bit-o-critter a little harder after everyone so quickly solved the Chrysaora.  Here's some cryptic hints for the three open rounds noone has guessed at yet:

Round 9 - One more than normal
Round 10 - Men are distinctly uncomfortable around this animal
Round 11 - This group not discovered until 1983

I will post the solutions when I get back to Atlanta tomorrow.

The Type Room

This is one of the rooms at AMNH where type series are kept, in this case for fish. A type series is that original set of specimens lodged at a museum when a new species is first described. These are therefore very valuable specimens, in a sense irreplaceable!  Its hard not to feel the gravitas of the mission of museums when faced with something as fundamental as a type series.  We also had a chance to see real coelacanths (they're bigger than I thought!), which was very exciting.

AMNH the reprise

It was a long but fantastic day at the Museum yesterday.  After Bento boxes with the grad studets, I met with folks from their comparative genomics and conservation genetics group including George Amato and Rob deSalle.  Then out for refreshments with the leech lab folks and their intrepid leader and old colleague of mine Mark Siddall. We gasbagged about everything from progressive metal to the latest leech they described, Tyranobdella rex, from up the nose of an unfortunate Peruvian child. What an awesome name. You can read more about it on Mark's blog Bdella Nea, linked from my blog roll somewhere hereabouts.
I didn't get to do everything on the agenda yesterday, so its back to the museum today to meet with people from Ichthyology and take a look at the fish type collection (drool). I might just snag some bit-o-critter pics from among the jars...

Bailer shells

Only at AMNH do they use bailer shells as chip bowls for doritos and salsa...
(don't worry, its not an accessioned specimen)

AMNH has the best view ever!

This is what the comparative genomics folks see out their windows...

AMNH Rocks

Seminar at AMNH went well. Now meeting with graduate students in the new graduate program in comparative biology.  What a great program and opportunity for students to take advantage of the collection and curatorial staff. Makes me kinda jealous.

Even though its a thoroughly modern museum, The place still smells of mothballs and that makes me smile.