I arrived during the big transit strike, so the Métro was not an option. Instead we got around the city (as freezing cold as it was!) using the fancy velib system. Locals and tourists (if they can figure out the registration process) can check out bikes from any of dozens of stations, ride them across town, and return them at a site near their destination. This was a fun and convenient way to get around and learn a bit about the environs, rather than emerging blinky-eyed from a subterranean cavern.

Paris is certainly a beautiful city, although the ubiquitous cigarettes seem to be considered invisible and biodegradable.

One of the motivations for making the trek to the exhibit was the chance to see some of my photos used as advertisements on the Métro walls. I was imagining a little poster-sized version, so I was stunned to see them blown up about 200 times larger than life, in gilded frames at several of the stations. Because most trains weren’t running when I was there, I didn’t actually spot one of the posters until my last night in the city. I set up to take a photo (above) and my camera battery died after a single shot! I took several mental photos and headed home.

The exhibit is being hosted in the Natural History museum, on the grounds of the Botanical Gardens. It makes for a nice walk in the afternoon sun.

Claire and her colleague Sara worked feverishly into the night preparing captions and content for the exhibition. Their office was in the top floor of the Geology Hall, so it was a common site to see the lonely glow from their skylight against the night sky.

The banner showing Peter Batson’s photo of a cranchiid squid, which also graces the cover of the book.

One of the unique things about the exhibit is that there are specimens of actual deep-sea organisms, in addition to the photos and video. The museum’s taxidermist Christophe was more used to working with animals that have fur and feathers, but he applied his tricks of the trade to marine animals with skill and enthusiasm.

Christophe’s son and the museum’s other taxidermists had to build all of the tanks that were used in the exhibit. Animals were suspended by fine transparent line in natural postures — painstaking work when they have to be positioned in liquid.

The displays are a mixture of photos (above and below) and actual organisms (the line in the middle). Photos were grouped by theme and habit, with the “red zone” shown above. In the large format pictures, we could see details in our own pictures that were never apparent in the small prints we were used to looking at.

Some of the smaller organisms were housed in tanks that line the wall. Originally, the tanks were just sitting there, brightly lit in the wall. This is where David Shale, Sara, Claire’s friend Sabine, and I stepped in. We went and got black foam-core and matte-board and started cutting masks and light blockers to generate an eerie deep-sea light. Since David is a professional photographer, the analogy that came to mind is that lighting can make or break a photo. We wanted these animals — plucked to the surface from thousands of meters deep — to get the visual presentation that they deserved.

I think the organism tanks look a lot more dramatic after being “blacked out”. My favorite are some radiolarians (technically now cercozoans) — deep-sea amoebae who live in intricate glass lattice capsules. We collected these from about 1200 meters and embedded them directly in transparent resin.

The “black zone” with darkened tanks and a couple of scary looking deep-sea animals. The fish would fit easily in the palm of your hand, and the medusa on the right is about the size of your fingertip.

Another perk of having your photos used in an exhibition is that they make postcards of them! I hope that people can take a bit of the mystery of the deep sea with them when they leave the gallery. If you are in France before May 8th, you should go by and check it out. You won’t see anything like it anywhere else.

Try shining one of those blue keychain LEDs around your house and yard, while looking through a pair of yellow-lensed sunglasses (to block out the blue light and make the fluorescence more visible). Check out the mustard in the cupboard, and some white laundry.

Many animals have fluorescent structures; some of these have obvious functions, and others are there for unknown reasons, or they may fluoresce just as a side-effect of other chemical properties. One of the most famous molecules around (yes, there are famous molecules) is the green-fluorescent protein (GFP). What makes this protein so amazing is that you can put the gene (DNA sequence) that codes for it into just about anything, and when that organism or cell pumps out the protein, it becomes brightly fluorescent.

The gene for GFP was first pulled out of the jellyfish Aequorea victoria [LEFT]. Later, using specimens bought at a Russian aquarium store, Mikhail Matz and his colleagues showed that corals also use a gene very similar to GFP to make green, yellow, and red fluorescence(1).

Now, about 100 fluorescent proteins (FPs) are known, and with this palette of colors at their disposal, biotech researchers are able to “paint” inside living organisms. With different colors, it possible to highlight (literally) two or three internal structures of interest, whether they are neurons or tumors, and follow their development over time, peeking inside without necessarily having to do a dissection.

One recent application of this fluorescent paintbox is both ridiculous and sublime: Jean Livet, Jeff Lichtman(2) and colleagues used fluorescent proteins to create multi-colored images of the neurons in a mouse brain. By using three or more FPs in combination, they claim to be able to produce up to 90 different tints (practically, maybe a dozen colors can be readily distinguished).

New fluorescent proteins are being discovered all the time, mostly from corals — not surprising since one piece of coral tissue may contain six or more different FP genes. Following the discovery in corals, FPs were found in copepods, little bug-like crustaceans that are like the insects of the sea. Now in October 2007, even more recently fluorescent proteins are making the news again with their discovery by Dimitri Deheyn and his colleagues in a strange organism called amphioxus.

Although they look like little eyeless fishes, amphioxus, or lancelets, are invertebrates. They don’t have a backbone, just a neural tube like the one in our spine. Thus they are one of the invertebrates that are closest to vertebrates — a far cry from a coral or jellyfish. It is not at all clear what function the fluorescence is serving in these animals, which spend most of their time burrowed in the sand.

So now FPs are known from cnidarians, near the base of the animal tree of life, and from amphioxus, lying on a remote branch. Because their DNA sequences are so similar, the chance that these fluorescent proteins evolved totally independently is vanishingly small. What this means is that there is a common evolutionary “ancestor” to the FP gene that is likely to be found across the animal kingdom. We should expect to discover more fluorescent proteins in ever more unlikely organisms.

How the gene was found in amphioxus is interesting in itself: As with corals, the fluorescence of amphioxus had been known for a long time, but nobody knew what caused it. Deheyn used the DNA sequence of a fluorescent protein from a coral, and searched for similar genes in amphioxus genome, which is publicly available online. Armchair science at its finest. (Of course, they went on to do many further experiments.) This is something that a student could do, given the right amount of insight and creative thinking! In fact, in a future report, I’ll describe how to search the growing number of available genomes to make your own amazing discoveries.

Footnotes ———————

(1) One interesting aspect of this discovery is that scientists had known about the fluorescence of corals for about 50 years, and had the GFP sequence for 15 years, before the connection between the two was made. Lesson: nothing is too obvious to be true.

(2) I know I am not in a position to point out amusing connections between names and careers, but “Light-man” does seem appropriate for this particular study.

The environmental influence of the fires, beyond the charred ground left behind, was impressive: I measured the area covered by the heavy white smoke in this satellite image as about 168,000 square km (41 million acres). Moderate smoke covers at least 600,000 sq. km (~232,000 sq. mi; 60M hectares), and it stretches offshore more than 950 km (almost 600 miles).

Given their scale, what long-term effects might such fires have on the oceans?

In one week, these Southern California fires were estimated to have released 7.9 million metric tons of carbon dioxide. About 5% of that amount would have been released as ash [ref]. Upon entering the ocean, these sooty particulates can have many effects, potentially both increasing or decreasing productivity via shading, sedimentation, adsorbing molecules, decreased albedo (less light reflection), and the input of nutrients. In one study, smoke from fires was implicated in a large coral reef die-off. The authors speculate that iron, a nutrient that can stimulate growth in trace amounts, was deposited with the soot, leading to an algal red tide and coral asphyxiation. Who needs butterfly wings when you have a raging inferno?

Once the rains begin, the increased ash and silt in runoff entering the ocean will give the fire another chance to affect marine ecosystems, potentially interfering with benthic filter-feeders, altering productivity, tweaking kelp forest dynamics, and annoying surfers. It will be interesting to monitor the residual effects through the coming year and beyond.

While the local marine impact remains to be seen, in a global context, the environmental effects of these episodic fires may be relatively minor: smoke regularly clouds the skies over large parts of Brazil and Indonesia.

As distinct as the elements seem, there is no way to escape the many interconnections between them.

This region is presented in a variety of ways by the media. A positive example is the stunning book The Deep. This surprise best-seller was a labor of love put together by Claire Nouvian after she became entranced by the deep.

Other examples may be less inspiring (and probably more typical). An article in WIRED magazine a couple years ago attempted to educate people about “What’s down there.” They highlighted factoids mainly about dolphins, turtles, seals, whales, and humans –– charismatic air-breathing vertebrates that make brief forays into the deep, but which can’t truly be considered inhabitants.

The article was accompanied by a fanciful illustration (below, left) that looks nothing like our currently-held view of deep-sea inhabitants (one example, below at right).

If they had done some more research, they might have discovered that the truth about the deep-sea really is stranger than anything they could have dreamed up. It is full of goggle-eyed squids, silicon-based “buckyballs” (radiolarians), forty-meter-long curtains of stinging death (siphonophores), and glowing jellies that propel themselves with eyelash-like paddles (ctenophores). These invertebrate predators dominate deep-sea ecosystems but observing them requires NASA-like efforts and technology.

In a way, by completely missing the boat, the article perfectly illustrated the point: we’ve barely scratched the surface in getting the public and the media to understand the deep ocean’s inhabitants.

-Steve

* Links to the WIRED article and the Johnsen article