Wednesday, March 28, 2012

To go where no (solo) man has gone before

Day late and dollar short, but it had to be included. I would have posted earlier, as the tweets came in from the initial launch to hitting the bottom, but I was cloistered in a hotel room with no internet access and a computer on the edge of failure followed by two days of interviewing. It was nice to be at a oceanographic research institution for the event, especially one with such a rich deep sea community. This meant that some of my meetings were cut short by calls to the press all over the world, but also that I got to hear inside discussion about the engineering, observations, and what it could mean for our business. So what was all the racket about? JC hitting the bottom.

Photo by (c)Mark Thiessen/National Geographic.
Deep Sea Challenge
Whether driven by pride or science and exploration, you have to applaud James Cameron's descent to the bottom of the Mariana Trench. It took guts, bravado, and a significant chunk of change. Even if he didn't find anything particularly new, and the 'spoils' aren't all reveled yet, the excitement and media attention he can and did generate has brought ocean research and exploration to the forefront of many people's minds. A handful of young children may have gained the excitement that Jacques Cousteau generated in previous generations. In the end, science needs and should want the public support - for funding, for purpose, and for a bright next generation of scientists.

I've been out to sea with Cameron for a month on a Russian ship, diving on hydrothermal vents as a scouting cruise for Aliens of the Deep. Since I wasn't actually working for him, I saw less of the exacting and demanding hollywood producer and more of an explorer. Many a night was spent on the aft deck with a delicious bottle of wine discussing science and telling stories. He has a very passionate scientific mind. You can see this in his movies, which almost always contain science fiction, a keen sense of exploration, and the ocean. Avatar, though terrestrial or extra-terrestrial, contained life that resembled and bioluminesced like creatures inhabiting coral reefs. Titanic, he claims was, at least in part, driven by his desire to dive on the wreck of Titanic. Which he did for the movie using his director's retainer money, to move finely explore and image the wreck than ever before with custom ROVs (remotely operated vehicles - remote underwater robots). He was pushing forward ocean engineering over a decade ago.

(c) Woods Hole Oceanographic Institution
So it was no real surprise that his sub design was innovative - resembling more of a spar buoy, meant to go up and down, rather than a more traditional submersible design. (Compare images of Deep Challenger and the US's workhorse Alvin.) As such, it seemed to have rocketed to the seafloor and back to the surface, allowing for more time on the bottom. Key to that may have been the titanium sphere - something only someone like JC could afford. I would have felt more comfortable going down in a titanium sphere than some of the other 'competing' designs, with a glass or acrylic sphere. The view might be better, but the probability of failure would have put a dent in my comfort and anxiety level during viewing.

My one complaint to Cameron is that he didn't make it much of a race. There was starting to be some hype about a 'Race to the Deep' - Cameron, Richard Branson, Sylvia Earle, and a commercial company. In the end, the other competitors haven't even made it to the starting line. While they unveiled sub plans, Cameron debuted the completed sub and started on an impressive test dive. A longer and more competitive 'race' would have heightened public awareness and kept this in the media spotlight longer.

Still it is a historic achievement and an advancement for science. Thank you Jim for your continued love and passion for the ocean!

(c) National Geogrpahic
For more coverage of the historic dive, check out the timeline on DeepSeaNews and more from National Geographic, including this video below.

Wednesday, March 14, 2012

DC in colorful bloom

Back from a brief respite in Hawaii. One might think coming back to DC in March would be tough, however the weather is almost better here in DC! Its been a gorgeous spring week, yet I'm happy to be inside. This has been a rare 2 week stint with no traveling for interviews or work. I'm finally back at the bench (and computer) to finish analyzing experiments and start new ones.

I also got result back from my first nanostring experiment. Nanostring is a new technology that directly counts individual molecules of mRNA. This means no bias from amplification nor making cDNA. The technology achieves this amazing feat by using a two probe per gene system. One gene-specific probe has a biotin anchor. The other probe has a unique fluorescent barcode - i.e. red-orange-green-orange-yellow or yellow-blue-red-red-green, etc. The probes are mixed with the mRNA and then immobilized via the anchor on a substrate. The barcodes are all aligned in the same direction by a current. Then the sample can be imaged and counted.

Although the changes weren't big, I did get a couple of interesting genes whose expression was significantly correlated with changes in arm length. Again, showing the power of this technology. Too bad at least one of them was Wnt-signalling related. Everyone in the lab is working on a Wnt (some on the same Wnt). I've flat out refused up until now... Wnt signaling is crazy complicated and still really controversial. It looks like I might have to finally dive into the mess.

(I am not related to Nanostring Technology, Inc and have only used their product once. I have yet to verify the results using qPCR and/or in situ hybridization.)