into the deep

Friend of the Blog (FOB) Tom Levenson over at Inverse Square has tagged Jen-Luc Piquant with a meme for the chronically narcissistic and self-absorbed: naming six random things about yourself that are not widely known. Nothing delights her more than expounding upon the subject of her glorious pixelated self — this is an avatar who scored off the charts on a narcissism quiz, after all — so Jen-Luc is delighted to offer these six personal tidbits to her fans out there in the blogosphere:

1. Jen-Luc has a mega-crush on the Spousal Unit's Second Life avatar, Seamus Tomorrow. She has seriously considered joining Second Life herself, in order to cyber-stalk Seamus more properly, except apparently the surname "Piquant" is not one of the options in that virtual world. (Hint, hint.) She could always join the "Tomorrow" clan but that would make her and Seamus related, dashing her romantic hopes from the outset. So for now, she pines from afar.

2. Jen-Luc is responsible for Sarah Palin's $150,000 shopping spree, having served as her personal cyber-stylist. She is non-partisan in her quest to bring haute couture to the needy — Joe the Plumber totally needs a makeover; Armani could do wonders for him — and besides, Nicole Wallace asked very nicely. You can't go on national television wearing clothes from a consignment shop. As for the RNC's insistence that the clothing will be donated to "charity," Jen-Luc hopes that's a euphemism for her sweet Cyber-self. She was promised the clothing once the election was over in exchange for her fashionista services. Every avatar has her price, and she covets that Louis Vuitton bag little Piper's been hauling around.

3. Jen-Luc secretly admires 18th-century French assassin Marie-Charlotte Corday for the sheer chutzpah of walking into Marat's private home and murdering the lecherous revolutionary in his bath.

4. Her trademark black French beret was actually manufactured in Taiwan.

5. Yes, that is her "real" hair color. Purple hair runs in the Piquant family tree.

6. Jen-Luc is secretly hatching a nefarious plot to hack into electronic voting machines on election day to vote herself into the Oval Office as a write-in candidate. Talk about an upset! Her first act as president will be to amend the constitution to insure equal rights for avatars. She thinks it will appeal to all those voters in Second Life. Perhaps then Seamus Tomorrow will notice her, and agree to be the First Cyber-Dude.

There you go! Meme accomplished! Jen-Luc is far too self-absorbed to tag six others in turn; as far as she's concerned, all Internet memes reach their zenith with her, and thereafter cease to be relevant. But perhaps her new party "guests" might choose to weigh in at some point, by way of introduction.

And now, it is time to move on to actual science — remember science? I've been completely immersed in the stuff of late, and finally have time to write about it. Just prior to the NASW meeting, I was in Boston for the annual Industrial Physics Forum (my bloggy musings-for-hire can be found here), focusing this year on frontiers in imaging ("from the cosmos to nano"). I especially enjoyed the session on marine and terrestrial imaging, perhaps because it's not something I write about very often. Or maybe it's just because two of the talks were about fluorescent coral and other examples of bioluminescent ocean creatures, each featuring lots of pretty pictures. That always livens things up a bit. A couple of years ago, I blogged about Bob the Hawaiian Bobtail squid:

He's a nocturnal creature at heart, and doesn't really need the sun, since he has a natural glow about him. Literally. He has a built-in flashlight to help him navigate those murky nighttime waters, hunt for prey, and hide from predators in turn. It's a special organ on his underside, a convenient little cavity that serves a dual purpose as home to colonies of a specific species of bacteria, Vibrio fischeri.

The cavity organ is lined with threadlike cilia that sweep bacteria from the surrounding water into the cavity, and the bacteria, ever adaptable, busily set up their own little colony. Once that colony reaches "critical mass," they emit the telltale glow. The glowing bacteria are surrounded by stacks of reflective plates to focus the light outward. That light helps Bob hunt for prey in dark waters. It also provides camouflage from any organisms trying to eat him, because Bob doesn't cast that telltale shadow on the ocean floor as a result of the moon's rays shining down into the water. Bob can even control the "wattage" of his bio-flashlight, simply by limiting the amount of oxygen that reaches the cavity organ. (The bacteria need lots of oxygen for the chemical reaction that produces the light.)

Large concentrations of bioluminescent bacteria are also, it seems, behind an ocean phenomenon called the "Milky Seas": glowing white patches of sea water stretching across an expanse as large as Hawaii. It's the stuff of urban legend, a rare occurrence that has mystified mariners for over 400 years. Certain algae have this ability, too. According to Edie Widder, a scientist with the Ocean Research and Conservation Association in Fort Pierce, Florida, the ancient Polynesians may have used the phenomenon of bioluminescence as a navigational aid — yes, just like Tom Hanks' character in Apollo 13, regaling an interviewer about the time his instruments malfunctions during a flight and he followed the trail of fluorescing algae churned up in the wake of his air craft carrier to land safely.

The point is, the ocean environment is filled with light, not just from jellyfish, but also coral, some fish, some shells, bristleworms, and crabs. "Almost everything down there makes light, for different reasons," says Widder. In 1960, Jacques Piccard and Donald Walsh dove to the bottom of the Mariana trend — some 35,797 feet deep –in a bathysphere to witness bioluminescence in action. It's pretty dark at those depths, but nonetheless, they reported seeing fish with eyes. That bioluminescent glow turns out to be darned useful for organisms in the murky depths, which seem to employ it for a wide range of purposes.

In 1887, Rafael Dubois began studying clams and discovered a class of organic molecules called luciferins, found in many marine creatures that glow when stimulated or agitated in some way. But the really exciting discovery occurred in the mid-1950s, when young Japanese grad student named Osamu Shimomura was assigned the thankless task of figuring out what made the remains of a crushed mollusk (Cypridina) glow whenever it was moistened with water.  A leading US group had been trying for years to do just that, and failed, but in 1956 Shimomura succeeded in isolating a protein that glowed 37,000 times more brightly than the crushed mollusk from which it had been extracted. Nagoya University awarded him a PhD in gratitude, and he set off to join the Princeton faculty in the US.

That's where Shimomura stated studying another naturally luminescent creature, the jellyfish known as Aequorea victoria, which evinced a green glow around its outer edge when agitated. He and his Princeton colleague, Frank Johnson, spent the summer of 1961 gathering jellyfish, cutting off their edges and pressing them through a filter to get a "squeezate." This didn't seem to be all that interesting at first, until one day when Shimomura poured some of the squeezate into a sink containing seawater. It flashed brightly! He realized the calcium ions in the seawater were causing a chemical reaction. The odd thing was that the light wasn't green — the color the jellyfish glows — but blue. Eventually they managed to purify the material and they named the protein aequorin.

Most of you have probably heard by now that Shimomura was a co-recipient of this year's Nobel Prize in Chemistry for his discovery of a different protein they'd managed to isolate, one that glowed green in sunlight, yellow under a light bulb, and fluorescent green under UV light. This became known as green fluorescent protein (GFP). By the 1970s, Shimomura had figured out that GFP contains a special chromophore that absorbs and emits light. Shining UV or blue light on the chromophore causes it to absorb the energy, become excited, and then emit the excess energy as light — and this process transforms the blue light from the aequorin into green light, which is why the jelly fish and isolated aequorin glow in different colors.

GFP has since become a standard tool for researchers all over the globe, enabling them to study biological processes previously invisible to the naked eye at the cellular level. (They use GFP as a tagging material.) While GFP was first isolated from a jellyfish, a substantial fraction of the stuff used in labs these days is derived from coral reefs. Coral, too, can fluoresce very prettily for the camera, in a wide range of hues, and the proteins that cause this are in the same family as GFP, according to Charles Mazel of Physical Sciences, Inc. in Boston.

Mazel spent years making night-time dives to photograph coral reefs under UV light, armed with little more than an LED flashlight and a barrier filter fitted over his diving mask to block out any ambient light that would otherwise backscatter and ruin the image.

Eventually, with the dawn of the digital camera and the ability to limit exposure times, Mazel discovered that he didn't need to dive in the dark anymore. He realized that the creatures' fluorescence was all happening whenever the flash went off, and focusing on just that moment also removed the ambient light effects, without special shading. Voila! Now he could photograph coral reefs 24/7! In fact, it's something of a hobby for many amateur aquarium enthusiasts, who keep sending Mazel their own stunning pix.

Thanks to advances in fluorescent imaging, scientists are learning a lot more about its significance in the marine environment, according to Mazel, mostly because of the superior contrast and level of detail gained from the technique. It's possible to tell the difference between various species of coral, for example, and between the coral and the symbiotic algae that live inside them, doing their bit to keep the food coming via photosynthesis. Also, "Little things that are difficult to see in natural light in a complex marine environment can be seen quite easily under fluorescence," says Mazel — things like baby coral polyps, a strong indicator of the overall health of a coral reef. "Juvenile corals are very small — on the order of 1 millimeter — and are next to impossible to find in the complex surroundings of a reef," he says. "By diving at night with the right equipment, many of these small corals can be excited to glow brightly, making them easy to find against the darker background."

One question that hasn't yet been answered is what function fluorescence in coral reefs is supposed to play biologically — although hypotheses abound. Maybe its purpose is to help capture light on behalf of the symbiotic algae so they can more efficiently go about their photosynthetic business, or perhaps it's meant as a sort of "sunscreen" to protect the algae from excess light. Mazel doesn't think either of those is likely — or at least not exclusive explanations. There's even some evidence that fluorescence could play a role in coral spawning behavior.

Marine organisms most likely fluoresce for lots of different reasons, as Mazel discovered when he took his passion for marine fluorescence to the deep sea. He mounted a UV light on a submersible manned vehicle and descended 3000 feet, where he spotted a fluorescent sea anemone, a lizard fish, and snagged a first look at a fluorescent shark. A manta shrimp with fluorescent spots appeared to use them as part of its threat display — a defensive maneuver to warn off predators. I wouldn't mess with the manta shrimp if I were a fish, however; aquarium owners know all too well that a manta shrimp will rapidly kill everything else in your tank. 

So, there are very definite survival advantages to be gained from bioluminescence, which might be why, as Widder maintains, the ability has evolved "more than 40 separate times" over the course of evolutionary history in various creatures. Creatures use it to attract mates or prey, to warn off other predators, as camouflage, or as a blinding attack display, never mind the relatively mundane purpose of getting a bit ambient light for better navigation.

As a grad student, Widder was measuring the electrical activity that triggers bioluminescent displays in dinoflagellates when her thesis advisor assigned her to develop an instrument for measuring the color of the very dim flashes of light associated with the phenomenon. She eventually became the lab expert with the High Intake Defined Excitation Bathyphotometer (HIDEX-BP), a technology also used by the military for missile defense, and got to tag along on some actual exploratory field missions aboard marine biology trawlers. This led to her association with a research cruise organized by the Monterey Bay Aquarium Research Institute (MBARI) to test a new type of diving suit called WASP. The suit features a display of various dials, switches and gauges in front of the diver's face to so s/he can monitor things in real time.

Anyway, Widder got to make several dives in WASP, and became hooked on the strange, eerie beauty of these glowing creatures of the deep. Her very first dive  in WASP was to 800 feet; she turned out the lights and expected to see a little bioluminescence. Instead, "There were explosions of light everywhere, like being in the middle of a silent fireworks display." And these creatures are capable of emitting quite a bit of light, too, not just very faint glows. On another dive, Widder was deep enough that almost no sunlight seeped down through the water, when suddenly her surroundings exploded with blue light. "It was so bright I could see all the dials and gauges inside the suit without a flashlight," she told PBS. "I had brushed against one end of a siphonophore chain, a colony of jellyfish more than 30 feet long. By bumping it I had stimulated its bioluminescence."

After numerous dives in WASP and other submersibles, Widden still wondered what sorts of creatures and behaviors still eluded observation because the bright lights and loud thrusters of the equipment scared them away. So she scrounged together enough components and funding to built the Eye in the Sea, a passive camera/observational platform that just sits quietly at the bottom of the ocean recording whatever creatures happen to pass by, and occasionally activating an "electronic jellyfish" lure — a blue LED light programmed to repeat certain display patterns when activated — to test Widder's hypothesis that bioluminescence might, among other things, prove very attractive to large predators. One species of deep sea jellyfish, Atolla Wyvillei, apparently uses bioluminescence as a sort of "burglar alarm" display — the idea being that, if it is attacked, its display would attract an even larger predator to attack the attacker, enabling the jellyfish to swim away. 

She tested it for the first time in 2004 in the Gulf of Mexico's brine pool, where methane bubbles up from the bottom providing food for the various mussels, clams and other organisms along that short. The camera was left on the edge of the shore overnight.

Not much happened the first four hours: just a lot of fish swimming by, blissfully unaware of the alien camera in their midst. Then the electronic jellyfish was activated. "Just 86 seconds after it went into its pinwheel display mode, I recorded a squid over six feet long — a squid so new to science that it cannot be placed in any known scientific family," she said. Clearly, it was looking for prey. "I couldn't have asked for a better proof of concept."

Next she took the Eye In The Sea (EITS) system to the Bahamas. Even though she was only able to deploy the system three times during the nine-day cruise — hers was not the only experiment being done — nonetheless her team observed nine different species of deep-sea shark, and even recorded a giant six-gill shark rotting around in the ocean floor sediment looking for pill bugs — a behavior scientists hadn't known about previously. She's now teaming up again with MBARI for Eye In The Sky on MARS (Monterey Accelerated Research System), which will install the camera system along MBARI's cabled network in Monterey Canyon off the coast to operate 24/7. "Instead of brief and infrequent glimpses, we are going to have a window into the deep sea that will be open around the clock, for months at a time," she said.

There's even an unexpected physics angle to bioluminescence (apart from the whole where-light-comes-from-atomically bit): there are two underwater neutrino telescopes being developed: NESTOR, in the Ionian Sea, and ANTARES, at the bottom of the Mediterranean sea. Widder was surprised to get a call from a distressed astrophysicist during a test run of the photomultiplier tubes designed to pick up the telltale flashes of light — known as Cherenkov radiation — that indicate the presence of neutrinos.

He asked her how prevalent bioluminescence in marine creatures was, and she informed him — to his chagrin — that it was "everywhere in the deep ocean, and you can't turn it off." Apparently they were expecting things to be a bit darker and less "photonically active," shall we say, and were surprised to find all that bioluminescence interfering with their ultra-sensitive instruments. The good news, says Widder, is that "There is no way it could be mistaken for Cherenkov radiation." Still, it was no doubt irritating; unexpected developments always are.

A few months later, Widder was surprised to read an article announcing the "surprising discovery" of bioluminescence in the deep ocean — even though marine biologists have known about, and studied the phenomenon, for decades. See, this is why interdisciplinary collaborations and communication is so very important. Hopefully the two fields will have a jolly time swapping data and observations over the coming years, enabling us to learn more about deep sea creatures, bioluminescence, neutrinos, and perhaps an unsuspected discovery or two, along the way.