Down, down, deeper and down

TL:DR – Deep-sea explorer Alvin is finally being laid to rest, so David Bradley salvages a few thoughts on deep-sea exploration from scientists who don’t seem to mind the pressure.


Alvin - Image from NOAAHow do scientists cope under pressure? In the depths of the ocean? In a place where the only natural light is the product of bioluminescence, where high-pressure sales has an altogether different meaning?

Plumbing the ocean depths began in earnest in the 1930s with the invention of the bathysphere. Built by New York explorers William Beebe and Otis Barton it was little more than a 2-tonne steel ball dangling from cables attached to a ship. Beebe and Barton dived to almost a kilometre below the surface off the coast of Bermuda in 1934 and piped details of their findings through a telephone to the crew up top. They reported sightings of fish and invertebrates the likes of which science had never seen before and have inspired a generation of scientists to explore deeper.

Paul Tyler of Southampton University’s Oceanography Centre is a marine biologist who regularly dives and has tried out all the deep-sea submersibles except the Japanese Shinkai craft. ‘It’s like sitting in a refrigerated VW Beetle without the seats,’ he told us, ‘there are normally three of you in a 2 metre sphere with three portals to look out of, as you get deeper you put more and more clothes on, but it’s fantastic, priceless’. But, a 4000m dive can take three hours to reach the seabed, ‘so you sleep, read, or chat, but once you reach the bottom, time flies past because you don’t want to waste a second, you’re so busy, you’re either collecting, photographing or setting up experiments,’ Tyler adds.

Even graduate students can go deep. Coral biologist Scott France of the College of Charleston made an early start in diving, ‘My PhD studies included research on dispersal of crustaceans between hydrothermal vents,’ he explains, ‘Within eight months of arriving at the Scripps Institution of Oceanography, I made a dive in Alvin to 3800 meters.’ Alvin is a submersible operating out of Woods Hole Oceanographic Institution. France realised that no amount of reading would have prepared him for the experience, ‘I was ecstatic,’ he exclaims, ‘I was an explorer venturing to a place on Earth that virtually no other human had seen before, witness to an environment completely alien to most people.’

For some the experience can be quite out of this world. ‘It takes a few hours to descend to the bottom and is very eerie,’ says Emma Jones a fish behaviourist at the FRS Marine Laboratory in Aberdeen, Scotland, ‘the sub tends to creak as it sinks which can be a bit disconcerting!’ She revisited a dead whale that had been ‘planted’ on the sea floor 18 months previously. ‘The skeleton was a very spooky sight,’ she says, ‘we were collecting bone samples to see what had colonized them, sediment samples, sucking up amphipods and filming.’
Submersibles are certainly not the most luxurious way to travel, says geologist Paul Aharon of The University of Alabama, Tuscaloosa who has just returned from the Atlantic diving in Alvin. ‘It is an uncomfortable ride inside the submersible with three people crammed in among the oxygen tanks, carbon dioxide scrubbers and electronic consoles,’ he explains. ‘Last dive I almost got hypothermia because I forgot to take long pants with me,’ he revealed to us, ‘I worked at 3 Celsius with no possibility of moving my legs for over 8 hours!’

He and Tyler also point out that there are some rather personal problems that face anyone on a submersible. ‘There is always the question of vital body functions such as urinating…’ Aharon muses, ‘In addition, the air we breathe has less oxygen and more CO2 than the atmosphere to prevent sudden ignitions. The results are headaches, memory lapses and slowdowns in brain functions.’

Alvin is a titanium-hulled submersible and can remain submerged for 10 hours under normal conditions, although its life support system will allow the sub and its occupants to remain underwater for 72 hours. It makes about 150 dives every year. There are several other equally adept submersibles including – Clelia and the Johnson Sea-Links I and II, which are run by Harbor Branch Oceanographic Institution. And, the Japanese craft Shinkai 6500, which weighs almost 26 tonnes and goes down, obviously, to a depth of 6500m. Shinkai, like the others, carries the requisite TV cameras, temperature and depth sensors, stills cameras and various navigational devices. But, riding Shinkai can be a lonely life since there is room for just one diver.

Discomfort aside, it is the wonder that keeps the scientists going back for more. ‘You don’t realise what a unique experience entering ‘inner space’ is,’ explains Tyler. ‘I went to Axial Seamount on the Juan de Fuca Ridge, which is actually the shallowest of my study sites, at about 1550 m,’ says Maia Tsurumi who works with Verena Tunnicliffe on hot vent ecology at the University of Victoria, ‘Getting to go down to the bottom in a sub was amazing – definitely one of the highlights of my grad career.’ The sites can be almost beyond belief, it seems, ‘The most fantastic biological site I have seen in my life is a tubeworm pillar,’ adds Tyler, ‘it is just unbelievable, 14 high and five meters in diameter, it’s just enormous covered in these tubeworms.’

In October, visual ecologist Tamara Frank of HBOI was about to set sail, when October’s Hurricane Iris and Tropical Storm Jerry scuppered her plans. She made her first dive in 1992, and is now studying the effects of light on the daytime depth distributions of organisms with colleague Edie Widder. Their dives need go no deeper than 1000m at the moment, but she is hoping to collect benthic animals too, which would mean much deeper dives. ‘Most dives in the submersible are fascinating, seeing these spectacular organisms in their natural habitat is just the most amazing experience in the world.’ she told us, ‘Once you pass through the air-water interface, you’re surrounded by seawater, and don’t even realize that you’re looking through a Plexiglas sphere because the refractive index of Plexiglas is the same as that of seawater…there’s none of this “looking out of little tiny portals” if you’re lucky enough to be in the front of the JSL; and the seats are very comfortable!’

‘There are too many rewards to count,’ Aharon also enthuses. ‘First, we descend for hours without lights to conserve electricity and you’ll see all kinds of eerie bioluminescence with psychedelic colours. It is a wonderful experience!’ he exclaims. ‘I wish I had more time to just sit and observe,’ laments Frank, ‘but on most of our dives in the Gulf of Maine, we immediately have to start transects, which are exhausting, because you’re straining to identify organisms that pass through the transect area as the sub goes through the water.’ She confesses that science sometimes obstructs the view! ‘Both Edie and I have seen beautiful gelatinous organisms during these transects, but couldn’t stop and film or observe them because data collection always has priority, and that’s sometimes frustrating.’ Takeshi Matsumoto of the Japan Marine Science and Technology Center (JAMSTEC) which operates the Shinkai submersible agrees that it is a busy game, ‘The most serious problem during a dive is the restriction of diving survey time,’ he explains, ‘observers have to accomplish everything within a few hours during the dive. Planning and preparation are essential.’ Jones agrees, ‘Because research vessels cost so much to run, and weather can change so quickly, you do feel you have to make use of every minute available to do your science.’

So, what is the motivation for cramming oneself into a tiny capsule and diving to the bottom of the sea? ‘I was always fascinated by the abyss and grabbed the opportunity when it came my way,’ Aharon told us, ‘I guess my initial attraction started in childhood when I read about Captain Nemo.’ Tsurumi agrees that the deep can affect you profoundly, ‘There is nothing so romantic and exciting as going somewhere seemingly totally inaccessible,’ she says. Aharon is totally hooked, ‘It’s an addiction, once you start going down (and hopefully, coming up again),’ he says.

It is not always so dreamy though. One of the more frustrating aspects of deep-sea science is not diving as Southampton University oceanographer Mark Varney explains, ‘I went on an expedition to the central Indian Ocean in June, and found the entire trip something of an ordeal. The weather was bad for most of the period, and the science wasn’t terribly successful.’

Indeed, extremely rough conditions are perhaps the worst aspect of doing research at sea. ‘On our Indian Ocean trip we were blown out on two occasions (to Indonesia and then towards Australia – both took several days to get back on to station,’ adds Varney. Tyler points out that, ‘Bad weather and very occasionally malfunctions are the only things that stop us diving.’ But, Frank notes, the hazards of diving are overrated, ‘I find it much more terrifying driving in Boston than diving in a submersible,’ she asserts, ‘At least in a submersible, you’re being ‘driven’ by a professional, there’s no ‘traffic’ to worry about, and you know the vehicle has been through an enormous number of safety checks.’

France too is not perturbed by the potential dangers, ‘My desire to see the deep sea and its organisms first hand represses rational consideration of the dangers involved,’ he says, ‘Of course there are dangers involved in travelling to such great depths. One can’t simply call for a tow-truck if the sub is stuck.’

‘The longest cruise I have been on was slightly over five weeks,’ says France, ‘and this was as a graduate student. At that time everything was an adventure and so the time passed quickly. Now that I am married, being away for that length of time would be an emotional hardship.’ However, at the end of a trip, the coming home can be a problem for some, ‘I often get “post cruise blues” after a cruise,’ admits Frank, ‘as do many of my colleagues, because you go from this exciting, noisy, “happening” environment, where there’s always someone to talk to, to a very quiet home.’

But, one question remains…how do they cope with those ‘personal’ problems during a dive? Jones had her own method, ‘I found out I was diving in Alvin at 4pm the day before so I deliberately stopped drinking any fluids from then on as I didn’t want to be squirming and crossing my legs for 10 hours,’ she says. Aharon, however, explains the standard approach, ‘We take capped bottles fitted specially for men and women. Not a pretty site, but we are all human.’

This article originally appeared in HMSBeagle, which has since sunk without trace…ironically enough, although it was fun while it was still afloat and is sadly missed by its trusty crew of writers and even those who had to swab the decks.

Also in Issue 75
The growing problem of biopiracy
Research assistants under contractual obligation

Previously, in Elemental Discoveries:
Accidents will happen
Predicting climate change
Green silicon production
P2P for scientists
Women in science
Academic poaching of researchers
Permanent implantable contact lenses
Profile of ETH Zurich
Paradoxical ozone

White Biotech

Is it just me or is the title of the latest paper published on Chemistry Central rather unfortunately politically incorrect when taken out of context? I suspect it is just me, as Google throws up almost half a million entries for “white biotechnology” and the phrase itself was apparently coined in 2003 or thereabouts.

Anyway, the paper’s full title is “Relevance of Chemistry to White Biotechnology” and it is authored by Munishwar Gupta and Smita Raghava of the Indian Institute of Technology in Delhi. They discuss the emergence of novel biotechnological approaches to the bulk production of fine chemicals, biofuels, and agricultural products. It is, as the authors say, “a truly multidisciplinary area” with “further progress depending critically on the role of chemists.” The authors outline the state of the art and in so doing hope to encourages chemists to take up some of the challenges thrown up by this area of chemical science.

You can read the pre-press version of the paper here (as a pdf).

Borromean Tales and Chemical Complexity

Fraser StoddartI got a chance to see pioneering supramolecular chemistry supremo, Professor Sir Fraser Stoddart of UCLA on the Cambridge leg of his UK tour on Monday. Sir Fraser took us on a whirlwind tour of the last quarter century of interlocking ring-shaped compounds, molecular dumbbells and the potential of collections of such entities to bring us the next generation of computer memory that could be fast, high density, and even error self-correcting.

He also took us on a spin through the synthetic tales of how to make Borromean rings on the molecular scale and ways to tie a Solomon knot with chemistry. It was visually and synthetically beautiful chemistry, told as eloquently and with the same dry wit as the last time I heard him speak. At that time he and his colleagues had designed the ultimate Olympic symbol from four interlocked molecular rings, something the UK’s Olympic designers should have perhaps taken to heart with their publicity materials.

However, aesthetics aside, Sir Fraser’s real take-home message is that chemistry is not yet the mature science many of its number would suggest. Over the last 150 years chemistry has gathered together many words and even begun putting them together into simple phrases, such as Sir Fraser’s own catenanes and rotaxanes. But, this maturity can be likened to the “maturity” of a toddler, he said. It is now time to stop trying to mimic nature with our chemical structures, turn up the complexity by at least an order of magnitude and Make, Measure and Model.

Did Strychnine Kill the Dinosaurs?

Strychnine structureStrychnine seems to be a commonly searched entry in the ChemSpider database. I am not sure whether that means there are poisoners among the users or whether it is people hoping to find out more about the recent case of a man accused of poisoning his neighbors’ dogs with a gopher bait pesticide containing strychnine. Alternatively, it could be people hoping to learn more about recent research into the unusual poses struck by dinosaur fossils.

Dinosaur fossils always seem to show the creatures “voguing”, as if there were some Jurassic equivalent of the 90s dance craze kicking off some time BC. But, the odd postures of these long-dead animals would actually suggest that they had an agonized death – the wide-open mouth, head thrown back and recurved tail – all point to poisoning, disease, or asphyxiation, according to two Berkeley paleontologists.

The usual explanation for the postures is that the dinosaurs simply died in water and currents dragged their bones into these odd positions and they were frozen in time as sediments settled and fossilization began.

Berkeley veterinarian-turned-paleontologist Cynthia Marshall Faux has seen a lot of animals that have been poisoned, hit by vehicles, or died of painful disease. They often arrive displaying the same postures as these fossils. She believes that the posturing dinosaurs may have met unnatural deaths, choking on volcanic ash, diseased, or poisoned.

The very same posture is seen in several disease states as well as in strychnine poisoning. Srtychnine is a highly bitter alkaloid found in several plant species, but it is its LD50 of approx. 10 mg per kilogram of body weight that points to its highly toxic nature. Strychnine causes muscular convulsions and eventually death through asphyxia or sheer exhaustion. Virtually all articulated fossils of Archaeopteryx have been found with the characteristic posture of the strychnine poisoned. We may never know exactly how these creatures died, but could it be that there was a dinosaur poisoner in the wild during the time of the dinosaurs?
InChI=1/C21H22N2O2/c24-18-10-16-19-13-9-17-21(6-7-22(17)11-12(13)5-8-25-16)14-3-1-2-4-15(14)23(18)20(19)21/h1-5,13,16-17,19-20H,6-11H2

Resistant to Base

It has been some time since we had a video interlude on Sciencebase, but I just could not resist this one. It’s definitely one for fans of the late, great Robert Palmer and synthetic organic chemists everywhere.

The lights are on, but you’re not home
You’re in the lab, work-ing alone
Your synthesis, is nearly done
Just add a chain to that car-bon

Don’t you know its resistant to base? The pH is past 14 and your stirring bar is dissol-ving! Dig those shoe covers and the impromptu appearance of a mop head. The only song in the world to rhyme potassium t-butoxide and ammonium hydroxide.

Thanks to Chemistry Central blog to bringing this one to our attention. Bryan Vickery has gathered together several chemistry covers on the site.

Funding the All-electric Aircraft

Superconducting motorToday, Philippe Masson of the FAMU-FSU College of Engineering and Center for Advanced Power Systems and colleagues at NASA and Georgia Tech publish details of an entirely new class of aircraft engine that, if it takes off, could lead to an all-electric aircraft that would cut airport pollution and reduce aircraft vapor trails to a distant memory. You can read my write-up about the work on the AlphaGalileo site here.

Unfortunately, while the science is sound, no one is yet beating a path to the inventors’ door, despite NASA backing. I asked Masson why he thought this was the case and his answer provides some cutting insights into the nature of the transport industry and the manufacturers that currently underpin it.

First off he pointed out that, “Conventional jet engines (turbofans) are very reliable and can still be improved: people are still working on NOx and noise reduction (including as part of our NASA sponsored project),” he says, “Therefore, there is a lot of inertia and imposing a new and totally different technology would be very difficult.” The major advantage of using electrical power is environment preservation because the performance of an all-electric aircraft would be unchanged unless one takes into account increased controllability and decreased maintenance requirements.

Masson’s electric jet is based on using zero-resistance superconducting materials as the magnetic components of the turbo-driving motor, but he points out that these, and cryogenic support systems needed to make them work, are still very expensive thus making funding difficult to find. It is possible that mass production would reduce costs to an economically viable level, but that is probably not going to happen any time soon.

“The motor designs we proposed can exhibit impressive power densities that would unfortunately almost only benefit airborne applications, there are no other applications with critical constraints in terms of weight and volume,” he told me, “As for the car industry in which combustion engine manufacturers are putting a lot of pressure to prevent new clean technologies to take off, jet engine manufacturers would not be happy to see electrical propulsion systems becoming a new standard.”

“An all-electric aircraft prototype is feasible,” he adds, “but imposing this technology as a replacement to gas turbines would still require a lot of research and development to meet flight requirements in terms of reliability.” However, Masson asserts that the appearance of increasingly electrical airliners from both Airbus and Boeing could hint at a future of all-electric aircraft. “I am convinced that one day in a not so far future we will see small electrically powered aircraft,” he says. He concedes that, “It will be years, probably tens of years, before we can see a truly all-electrical aircraft as all the components require extensive testing and a very high reliability before being implemented in airplanes.”

Masson and his colleagues have approached several companies and aircraft manufacturers and have not yet been successful in getting funding to build a prototype of their superconducting propulsion motor for which patents are pending. “We are still hopeful and will keep looking for funding,” he says.

Science in the Movies

Some time ago, I wrote a feature for the long since scuppered HMS Beagle on BioMedNet.com on the subject of science in the movies. I interviewed various scientists and people in the movie industry about the role of experts in advising on plot lines and details. It was quite a departure from the usual research reporting and was part of my once-monthly “Adapt or Die” column for the webzine. Sadly missed, for a short time, by many life scientists.

One thing that strikes me repeatedly is the lack of chemistry in the movies, other than the chemistry of weapons of mass destruction, of course. Carl Djerassi attempted to bring chemistry to the fore in his Nobel play, Oxygen, but that was a one-off and was in a sense a test-bed for his ethical and moral debates which he embeds in many of his science in fiction scripts. UPDATE: Of course, there was the wonderful Breaking Bad that came much later than this blog post from 2007!

Living Chirality

LeucineYet another possible explanation for the bias in life’s handedness – the fact that nature uses mainly only form of the building blocks of proteins – comes from Dutch chemists experimenting with the sublimation of amino acids.

Writing in the latest issue of my alma mater Chemical Communications, Ben Feringa and colleagues at the University of Groningen have demonstrated significant enantioenrichment of a variety of amino acids by sublimation in which preferential evaporation of the predominant enantiomer occurs from a mixture of low ee amino acids. They lay claim to this process as being a possible mechanism for the presence of ee of amino acids under the conditions found in space.

Theories abound as to why life on earth predominantly uses L amino acids. Most rely on some obscure initial set conditions and a convoluted route from a small excess in outer space to the seeding of amino acids on earth. While Feringa and colleagues discuss their findings in terms of interplanetary conditions it may be just as possible that their process had some counterpart on the primordial earth.

InChI=1/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/f/h8H

Thumbing Scientific Papers

A rather eye-catching paper was posted on the ChemRank site recently entitled: How to write consistently boring scientific literature. The paper is a parody on the art of writing a research paper by biologist Kaj Sand-Jensen of the University of Copenhagen. And begins, “Although scientists typically insist that their research is very exciting and adventurous when they talk to laymen and prospective students, the allure of this enthusiasm is too often lost in the predictable, stilted structure and language of their scientific publications. I present here, a top-10 list of recommendations for how to write consistently boring scientific publications. I then discuss why we should and how we could make these contributions more accessible and exciting.” Are you enticed by Sand-Jensen’s intro? Me neither. It just seems it would be as terse and as inaccessible to a lay reader as any of the papers he parodies. You can give it the thumbs up or the thumbs down on ChemRank.

Atomic Chips

Atomic chip schematicLaboratory spectrometers are great lumbering beasts, essentially tied to the bench and useless for slipping into an overnight bag and heading off for a spot of analytical field work. Thankfully researchers are working on changing all that, at least in the area of atomic spectroscopy.

Holger Schmidt of the University of California, Santa Cruz and Aaron Hawkins at Brigham Young University and their colleagues have found a way to build an atomic absorption spectrometer on a chip just a few centimetres across. I report on their work in more detail in the latest issue of SpectroscopyNOW.

Schmidt told me that the new instrument could be used not only in gas sensors and other portable analytical devices but also to stabilize the frequency of lasers and even in the future world of quantum information processing, which will revolutionize computing and telecommunications.

“Frequency stabilization could be implemented within a couple of years,” he says, “while quantum communications applications are definitely further out, at least ten years, that work is in the fundamental science stage which makes it very exciting for us.”