Monday, August 2, 2010

Deep Type Flow's big change

I am moving off Blogger and onto a dedicated domain, so from now on, you can join the discussion at   If you liked any of the old posts and don't want to lose them, fear not; I migrated them all to the new site too.  If you prefer to get your dose of bloggy goodness by RSS, the link for that is here.  If you were a Feedburner user, you'll probably get an email from me shortly with new details.

Thanks Blogger, its been real, but I think its time we saw other people...

Illustrated humour device succinctly encapsulates the dysfunctional paradigm of science communication

If you don't subscribe to Saturday Morning Breakfast Cereal, its well worth it.  Today they tackle jargon (click for the rest)

Thursday, July 29, 2010

The solution to Bit-o-Critter round 27

The last BoC was a triple header from previous winner Sarah F. and you had to get 2/3 scientific names correct.  David Gross was the first to do that, correctly identifying the first as a reticulated brittle star Ophionereis reticulata and the third as a flamingo tongue snail Cyphoma gibbosum

Nobody got the third one, which was a fireworm, Hermodice carunculata.  That's one of very few BoC's that has never been solved

If you have to go, go big!

When you want to learn about the biology of a charismatic species, any species really, sometimes you end up learning about the grosser side of life too.  Thats kind of how I came to take this picture last week in Mexico, where I and several others from the team at Georgia Aquarium have been doing research on whale sharks lately (see several other blog posts heareabouts).  It was taken during an aerial survey we did from an altitude of 1,500 ft in a Cessna 206 and shows a whale shark that has just defecated.  Now, whale sharks tend to do everything on a giant scale, so perhaps we shouldn't be too surprised, but I estimate the animal to be between 8 and 11m (25-35ft) in length and so, based on that estimate, thats a cloud of poo behind him thats over 30ft in diameter!  Its unusual to see wild sharks in the act of pooping, but this group of animals was so numerous and feeding so heavily, that you could actually see several clouds like this at any given time.  Whats feeding heavily got to do with it?  Well, unlike mammals, which tend to have a relatively fixed gut passage time for food, a lot of cold-blooded critters can, well, sort of push it out the back end, simply by pushing more in the front end.

Far from being a trivial observation of one of life's less savoury moments, it could actually become a really important research opportunity if we can manage to catch some of that magical egesta in a container of some sort, for analysis back at the lab.   Scientists can do all sorts of stuff with poo, like looking for parasite eggs or other pathogens, sequencing the DNA of both the shark and its prey species, or comparing nutrient values of food (from plankton tows) and comparing them to values from faeces to work out how much nutrition they are gaining from their food.  Its a great way to learn a lot in a short time and do it in a totally non-invasive way.

Mostly though, its a cool photo to gross people out at parties...

Monday, July 26, 2010

No ban for Southern New England lobstering

In an earlier post I mentioned a proposal to the Atlantic States Marine Fisheries Commission by its lobster science committee to ban lobstering in Southern New England (i.e. south of Cape Cod) for 5 years to allow the fishery to recover.  Not surprisingly, that proposal has been rejected.  An alternative motion proposing that the commission "consider" either a 75% cut in allowable landings, or a 50% cut, or no cut at all, was approved.  Well hey, thats a nice clear path forward now, isnt it?

These events continue to highlight the tremendous complexity and difficulty of successfully managing modern fisheries.  Its easy to blame the committee for being indecisive, but the truth is that when you're faced with making decisions about someone's livelihood, and they start using phrases like "The moratorium was the bullet in a gun that was pointed to our head," and "A poison pill has been put in front of us", then making decisions purely on the science isn't so easy.  This, then, is annoying to the scientists who work hard to provide the best evidence possible to help make good decisions, only to see their data dismissed or disregarded because of more anthropocentric considerations.  Throw in a healthy dose of regulatory red tape and the poor managers just can't win.

I guess its one of those situations where when everyone is miserable, you probably made the best decision, but it may well mean the slow death of a long-troubled fishery (no matter how rosy picture the fishers want to portray).  One day I expect to look back at this post and fondly remember when we had a lobster fishery south of Cape Cod.  On that day, the shifting baseline strikes again.

Thursday, July 22, 2010

Dancing with a Giant

A lot of people think science is soulless, sterile or austere in its objectivity; there’s a prevalent stereotype of the scientist as a lab nerd in a white coat, out of touch with the “real world” and with the more emotive aspects of life. That couldn’t be further from the truth, of course. Most scientists I know – me included - are motivated precisely by a profound wonder and amazement for the natural world around them; its usually why they get into science in the first place. When biologists go into the field, they often end up reconnecting with those feelings, established during their formative years, and end up resorting to a sort of childish state of pure joy over whatever biological phenomenon that they happen to be studying. I just had such an experience, one that was so extraordinary that it may well have changed the way I think about biology forever.

As part of the research program at Georgia Aquarium, we are in Mexico to study the biology of whale sharks, which gather annually in the coastal waters of Quintana Roo, from Isla Mujeres north and west to Isla Holbox. Its bliss just to be out on the water again (its been a while), admiring the everchanging seascape, marveling at the myriad forms of life that make their home in the ocean, and reminding yourself that the endless stream of doom and gloom news about “the environment” isn’t really the full picture. Flying fish skip from wave crest to wave crest, pursued by sinister-looking frigate birds that swoop in to grab them on the wing, while turtles lazily periscope their heads above the surface to spy on pods of spotted dolphins that race around as if there were somewhere important that they really needed to be.

In due time, we found our objective, a group of whale sharks feeding at the surface, attended by a flotilla of ecotourist boats. Each of our team had a chance to swim alongside these spectacular behemoths as they were cruising effortlessly among the boats and patches of food, at speeds that exhausted a mere human to match.  We also photographed many of them for an identification database.  Then we took some time to gather data on the physical and chemical properties of the water, during which the ecotour boats petered away, returning their cargo of tourists to their respective all-inclusives in time for lunch and leaving us with the whale sharks mostly to ourselves. They continued to feed, constantly inhaling bathtubs of plankton from the surface tension, their gills flapping loosely on the rejected water current like flags in a gentle breeze.

It was at this point that I got in the water a second time. Rafael, our captain and colleague from Project Domino, had put us on a large animal that was feeding below the surface in a more vertical pose than their normal surface “ram filtering” style. This more upright type of feeding, which they use when food is especially dense, sees their tail sink down towards the bottom and cease its rhythmic swinging and, hanging suspended like this, the animal begins to actively suck in enormous gulps of water. In this state I was able to approach the animal much more closely, a large male, and to see how each pulse of that fantastic mouth was pulling in not only water but tiny silver vortices of air down from the surface, such was the force of suction. He was suspended like this for what seemed like an eternity, but was realistically perhaps 15 or 20 minutes, during which he continued to feed and appeared completely indifferent to my presence. I was able to swim over every part of his massive frame and inspect every detail, from his tremendous girth to the creamy white belly distended with food, and from the remoras that pestered his every fin to the tiny copepod parasites grazing across his skin like herds of hoofstock might roam a savannah.  His body was home to a veritable community of hangers-on. I watched his eye roll carelessly over me while he continued to inhale vast amounts of water and plankton, all of which disappeared into that cavernous mouth with its 20 jet-black filtering pads. We continued to dance together like this – or rather I danced around him - close enough that I could have reached out to touch him at any point, until with a tiny shake of his head and a hefty sweep of his tail he was done with the meal and headed off in search of another patch to vacuum, leaving me breathless from a cocktail equal parts exertion and exhilaration.

Back on the boat I did my best to relay to the others what I had just experienced. Despite apparently talking “a mile a minute”, I struggled to find the right words, but they were probably unnecessary anyway. Certainly everyone who had been in the water with the animals that day had experienced many of the same feelings, and I am sure they were writ large on my face (in big black and white spotted letters!). In swimming with this one particular animal, I experienced a profound connection with a truly spectacular natural phenomenon, one that will provide ample motivation to continue the search for a better understanding of the nature of such things, for long into the future.  These are the moments that launch and tie together a career in biology, and that was the best one I have ever had.

Sunday, July 18, 2010

The latest from the Whale Shark Festival in Isla Mujeres

I am down here with other folks from the aquarium as well as other scientists, government folks and ecotour operators for the 3rd annual Whale Shark Festival in the beautiful Yucatan location of Isla Mujeres.  Here's some short videos that might give you the flavour of whats been going on.

Here's Beatrix and Rafael de la Parra from Proyecto Domino explaining the importance to Isla Mujeres of whale shark movements to and from Utila in Honduras.  The audience is mostly ecotour operators and members of the public.  Bob Hueter from Mote spoke about threats to whale sharks, while Darcy Bradley from ECOCEAN talked about their program and I chimed in for a talk on whale shark research at Georgia Aquarium

Check out this inflatable whale shark from the festival parade - that thing is made of awesome!  Later that night they illuminated it from the inside and it watched over the stage show and the Ms Whale Shark awards, where they elected a grandma as queen of the festival!

This is Teatro del Mar, and educational puppet show that Amigos de Isla Contoy have shown to thousands of school kids to improve ocean literacy.  The kids were completely rapt!

And I couldn't resist putting in this clip of turtle hatchlings at the state run hatchery in Isla Mujeres.  There's a lot of problems there with beach erosion and disturbance, so when turtles nest, they excavate the eggs and bring them to the hatchery, where they have a cool fenced off area where the eggs are reburied and incubated until they hatch.  Warning, cuteness overload a distinct possibility...

You can follow along on Twitter too

Friday, July 16, 2010

Play Bit-o-Critter Round 27 - new and improved!

There's a new Bit-o-Critter rule in play - if you get it right, you get to pick the next round animal(s) and stump your colleagues.  Here's Sarah F.'s trio of selections, which she picked as her reward for getting round 26 correct.  Scientific names please.  First person to get 2/3 correct in a single comment wins.

Thursday, July 15, 2010

Could it be? The END?

CNN is reporting that the new device put on the wellhead of the BP oil rig Deepwater Horizon appears to have stopped the leak and is holding under the pressure, at least for now.  Lets all cross fingers that this marks the end of major leaking into the Gulf of Mexico.

Fieldwork here we come!

Things will probably get a little irregular around here over the next couple of weeks.  I'm part of a group of Aquarium folks leaving for Mexico tomorrow to participate in the Whale Shark Festival on Isla Mujeres, just near Cancun, followed by some intensive field work with colleague Rafael de la Parra, who you may remember from previous posts.  We'll be tagging animals, photographing their spot patterns for the ECOCEAN project (their spots are like fingerprints!), collecting plankton samples and sampling the chemistry of the water to look for differences where they are feeding and where they are not.  I'll try to post some stuff as we go along, even if its only a picture or a video here and there (there wont be much time for writing, unless the weather closes us out)

All of this is part of our partnership called Project Domino, which aims to understand and protect whale sharks in Mexican waters.  Its bigger than that, however, because many of those same animals travel from the Yucatan to the Caribbean, the West Atlantic and the Gulf of Mexico; sharks dont pay attention to sovereign borders.  Obviously concerns are running high for any animals that travel into the GoM, due to the Deepwater Horizon disaster.  Keep your fingers crossed that those animals avoid the affected area and that this latest attempt to cap the wellhead is successful.

Okeanos footage

National Geographic is hosting some nice footage of a submarine volcano in Indonesia.  The video was gathered as part of the Okeanos Explorer and its current collaborative research cruise between NOAA and the Indonesian Government

The footage shows some impressive fields of stalked barnacles, an abundance of shrimp and some really cool sulfide chimneys and elemental sulfur flows.

Monday, July 12, 2010

Whats in a name? Origins of the word "shark"

To a recent roundup of whale shark news, I appended a sort of human interest one-liner about how “shark” is the only word in the English language that derives from a Yucatec (Mayan) Indian word – “Xoc” (pronounced like “shock”). It was just one of those factoid tidbits picked up somewhere along the line of life, maybe while working in Mexico, I don’t remember. It tickled some interest from blogger @hectocotyli on Twitter, who posted a follow-up tweet questioning whether this was actually true, and citing a paper by Tom Jones, from the 5th Palenque Roundtable in 1983. That paper is entirely devoted to the question of the origins of the word shark. I read it and was transported, what a great story! So here it is then, a deeper look at the origins of this word "shark", with thanks to @hectocotlyi for having an inquiring mind and for finding the paper.

According to Jones, the very first mention of the word shark in association with the animal for which we use the name today was in a 1668 work by John Wilkes. One of the first mentions of the word in a diuctionary, however,  is in an anonymous work from 1689, which defines a shark as a “shifting knave”. In other words, a crook, dodgy sort or general baddie. That was surprising to me, because I had just assumed that the use of shark for a shifty character was a much more modern one derived from the noun referring to the animal wif de big nasty teef. Bailey’s Dictionary in 1724 used “scearan” as the likely origin for the word: a saxon term meaning “cut to pieces”. Webster took a different tack in his 1828 dictionary, accepting a theory that it comes from the greek word “carcharias” (sharp tooth), even though that word clearly has a typical Greek hard c sound, not the soft start of shark. These days, Oxford English Dictionary just says “of obscure origin” and to me that might be the best answer, if you insist on a European etymology.

The major alternative explanation is that the word comes from the Yucatec Indian word “xoc”. Now, explaining what the word xoc means in Mayan is not as simple as it would be for European languages; Mayan language groups are apparently among the most arcane and problematic for linguists to study, especially for the bizarre glyphic written forms. Jones goes into the issues in great detail, and its a fascinating read, but I could summarise by saying that at best the word refers specifically to sharks as we know them, and at worst to an ill-defined group of toothy aquatic animals that might also include large fish, crocodiles and toothed whales, in both fresh and salt water. There’s lots of usage examples to support the idea that it means sharks, though, including “xoc yee halal” which are arrows with sharks teeth for points, and “uayab xoc” which is a sort of demon or were-shark, part man and part shark. Its not that simple though, because xoc can also mean “to count to” or to refer to dates ahead or behind. In Mayan glyphic writing, glyphs are apparently freely substituted for other words or parts of words that are pronounced in similar fashion, even though the agreed meaning of the glyphs (or bits of ther glyph, sort of like syllables) may be radically different, which really confuses the issue and is a big part of the reason why written Mayan took so long to decode. In the glyphs from the Jones paper shown below, for example, the middle glyph is a counting glyph with the same meaning as the one on the right, but incorporates the glyph for xoc, of which the stand alone version is shown on the left. To me another obvious clue here is that the glyph for xoc is the head and mouth of a beast, even when used to mean "to count",  which seems to fit well the definition in the broad sense. The beast even has a rostrum of sorts, and triangular teeth.

If the usage roughly matches, then, how would a Mayan word make it to English?  Given that the Spanish and Portuguese were in closer contact with the New World earlier than the English, why would English not pick up the Spanish “tiburón”.  Put another way, why does the Iberian word not also resemble “xoc”? If it’s true that shark is of Mayan origin, then it must be a standalone jump – somehow going from Yucatec to English, skipping Spanish and Portuguese.  For the etymologists, it seems that this lack of intermediate steps or of words that share the same origin, which they call “cognates”, is a real problem for accepting the Yucatec origin of “xoc”.

Jones proposes a way that this could have happened, on the expeditions of John Hawkins from England to the Caribbean in the late 1560’s (incidentally, Hawkins was a pioneer of the English slave trade). Further, Jones proposes that the critical moment may have been an unanticipated battle between Hawkins and some Spanish ships forced to share moorings near Campeche in 1569.  The fight resulted in the destruction of several vessels from both sides and some pretty heavy losses, with over 200 of the English eventually consolidating onto a single ship called the Judith and heading for home.  Jones suggests that a shark frenzy feeding on the unfortunate victims of the battle – and on those who died of hunger and disease on the crowded Judith over subsequent days - might have created an indelible impression on the English (only 15 of whom made it back to Cornwall), enough to cement in their lexicon the local name for these demons of the sea.

As a complete linguistic noob, I find the proposed Mayan origins of shark to be more plausible than the Greek or Saxon suggestions. More importantly, though, it’s a way better story, and when there’s that much uncertainty, I’ll always choose the explanation that involves the greater ration of mysterious glyphic languages and dramatic ship battles on the high seas, wouldn’t you?

Friday, July 9, 2010

Whats happening all the time in 90% of the oceans, and half the time in the other 10%

To explain the title a little better - most of the oceans are in total darkness all the time, and even the sunlit zone is an inky realm every night when our star visits the other side of the planet.  Accepting that we can't easily visit the bathypelagic zone (the deepest bits) without submersibles or ROV's (remotely operated vehicles), then perhaps the best feel we can get for what's happening in the vast majority of the oceans is to don SCUBA gear and dive the surface of the open ocean, but in the dark.  In preparation for doing a bit of that later this year, I've been looking at "black water night diving" stuff on YouTube.  Honestly, the idea invokes in me a healthy amount of fear, but if these videos are anything to go on, then I hope that will soon be replaced by wonderment and fascination.

Pelagic plankton. I love the flatfish at 0:28. If you know what the spongy looking thing at 1:40 and 4:04 is, please let me know.

Humboldt squids - I especially liked the face-on attack at 2:00 and the strobing at 2:30

I guess this is the most obvious anxiety. The one at 1:20 just gives me the heebie-jeebies!

This video isn't so much pelagic as reef, but the spawning sea cucumbers and then the palolo worms about 5:40 in are just great, and I love the music, which (curiously) is from that abysmal Mel Gibson flick Passion of the Christ.

Play Bit-o-Critter Round 26

OK folks, I'll take the genus name for organism in the top half of the photo, with a bonus for the other organism in the bottom half.  If you couldn't tell that this was two organisms, then there you go, I just gave you a hint. :-)

Thursday, July 8, 2010

The solution to Bit-o-Critter round 25

After some time, Sarah F. was able to get both of the Round 25 Bit-o-Critters.  Congrats, enjoy the warm inner glow of vanquishing your opponents.

25A was one of the more common salps, Salpa cylindrica.  As Sarah noted in her answer, salps are "pelagic tunicates that graze on phytoplankton. They can be found as asexual, solitary individuals or in long chains. Salps are also important in carbon cycling in the ocean."  One of the other cool things about salps is how they move; they're basically little jet engines.  The ridges you see along the body in the photo below are muscle bands that can be squeezed in sequence to push water through a central canal and jet them along through the water.  Some salps are surprisingly powerful swimmer.  Photo credit: Census of Marine Zooplankton

25B was a sea angel or Clione sp.  Even though they are about as far from snails as you can imagine, they are actually molluscs.  They're pteropods (= wing-foot), which is one of two groups of exclusively pelagic molluscs (the other being heteropods).  A photo doesn't do them justice, so instead enjoy this weird and mildly amusing Japanese video of a Clione gently swimming, and then violently attacking its lunch, to the tune of....well, just watch it and see...

If you have any idea what they are saying, I'd love to know...