You wait ages for a new ome to come along, and then you hear two in the same talk.

You wait ages for a new ome to come along, and then you hear two in the same talk.

First, there's the 'virhostome', which is short for virus-host interactome. This describes all the ways in which the proteins of a virus interact with those of its host. Effectively, viruses hack into the protein networks within the host cell, and take it over.

Natali Gulbahce combined (mashed up?) the virhostome for the Epstein Barr Virus with a gene-disease map to create what she calls the 'EBV diseasome network'. This gives a map of the interconnections between viruses, proteins, genes and diseases. It's a way to tie diseases to viruses – something we already have a pretty good idea of in this case, as the network approach basically recovered all the illnesses previously thought linked to EBV - and to get a handle on the mechanisms by which bugs cause bother.

She then took it to the population level, analysing medical records to compare the patterns of co-occurrence of the diseases of EBV – how many people with mononucleosis, for example, also get lymphoma? – with the positions in the network of the molecules behind them. Such diseases tend to be associated with nearby bits of the diseasome network.

Ultimately, Gulbahce told NetSci 08, besides revealing such patterns and aiding diagnosis, mapping these pathways might help us identify their weak spots – the parts of the virhostome or the links between genes and diseases most vulnerable to disruption. And it might help show how genetic variation contributes to different peoples' differing susceptibility to disease.

Posted by John Whitfield at 02:27 PM | Permalink

This is the first conference I've been to that makes me feel old. That's not because I'm getting older while grad students stay the same age. It's because much of the research deals with phenomena – Facebook! MySpace! iPhones! – that until now I've been more than happy to let pass me by. I'm used to feeling baffled in conference presentations, but not fusty; it's like being at a symposium on High School Musical.

But, of course, network science's bleeding-edgeness is what's brought me here (to NetSci 08 in Norwich). This is a discipline that didn't exist 20 years ago, and which is driven in large part by the digitization of everyday life, creating hard yet juicy data on our social lives the likes of which has never existed before.

Today's theme was 'Network theory and its applications to health and society'. Someone, can't remember who, once said that anything that calls itself a science, isn't. So: social science, political science – not. Biology, physics – are. But network, um, science is starting to make the social sciences more like the natural sciences (not everyone will think that a good thing, of course), thanks to its vast amounts of data, coupled with the solid mathematical foundations. Network maven Duncan Watts – formerly of Columbia, now Yahoo!'s head of social science – calls it Social Science 2.0.

Another thing that struck me was that network science lends itself to intuitive visual representations of complex ideas. You'd hope that would help get these ideas to policy-makers and the public. A case in point was a talk by Martin Newman at Michigan, on how you map social information onto real-world geography using cartograms (cool pictures here). Newman showed how this way of turning data into space can let you see whether, say, New York has more lung cancer than you'd expect, given its population (it doesn't), or Los Angeles more murders (it does).

Network studies are touching just about every discipline, because you can say general things about networks regardless of the players. They could be enzymes, genes, species in a food web, nerve cells, patients or their diseases, companies, politicians or countries. Plus the whole hard-core theoretical side of the discipline brings in the mathematicians, computer scientists and statisticial physicists. Besides being the hippest meeting I've been to, it's also the broadest. Tomorrow's theme is 'Planet Earth and it's Life'. Check back here to see what happens.

Posted by John Whitfield at 05:46 PM | Permalink

After getting the scoop of a lifetime last week – finding ice – Phoenix is now ready to start doing some experiments of the chemical kind (press release).

This is the first ever chemistry experiment to be done on polar Martian soil. But I don’t think Phoenix will be using pipettes and test tubes, or even a Bunsen burner.

Phoenix’s lab is called MECA (microscopy, electrochemistry and conductivity analyzer) and will be able to test the Martian soil’s acidity and salt content, and the instrument can also check out the different isotopes of elements present, and work out if there are any organics there.

So far, Phoenix has been digging and baking – but this foray into chemistry is a pretty exciting step forward in working out what it is really like up there.

Photo: NASA/JPL-Caltech/University of Arizona/Texas A&M University

Posted by Katharine Sanderson at 12:08 PM | Permalink

From the editors: Mars Phoenix scientists have finally confirmed finding ice at the landing site (watch the chunks sublimating in the lower left of the trench in the animated image below). Read our full story here. And for more on a new study about how volcanism and ice may have shaped Mars's northern regions, try this news story.

Posted by Alex Witze at 06:31 PM | Permalink | Comments (2) | TrackBacks (0)

The Phoenix mission scientists just won't call it ice. It's getting almost hilarious the way they assiduously avoid the term. On a conference call today, Ray Arvidson, the robotic arm lead scientist, talked about some of the features of a deep 5 to 7 centimeter trench. The trench combines "Goldilocks" and "Dodo" -- two shallower test trenches. You can see the ledge of exposed "light-toned" (as they call it) material in the upper part of the trench. You can also see a little tiny nugget of something -- don't say that word -- sitting just to the left of center in the trench.
So the team is going to watch what happens to these two features over time. The chunk, being small and exposed, would be expected to sublime and disappear over time. And the ledge, if it was an extension of the cold, thick ice table below, might actually be expected to accumulate frost. We'll see.
Bill Boyton, lede for the TEGA instrument, said the baking is going well -- they've performed two step-wise bakes, up to 175 degrees Celsius, without detecting anything other than carbon dioxide. In the next few days, he'll amp that oven up to 1000 degrees Celsius. That's when things will really start cooking.

Posted by Eric Hand at 09:32 PM | Permalink

Spending one week on board the CCGS Amundsen has been a humbling, inspiring, and altogether amazing experience for me. As I said before, it has been a great privilege, too – not even Nature’s science reporters often get to see spots as grandiose and pristine as the Canadian Arctic.

Change comes faster to this unique environment than most of us would have thought ten or twenty years ago. With climate change and global warming proceeding at an unexpected pace, it seems doubtful now if we can preserve even to the next generation the Arctic as we knew it.

It is important that scientists bring this unconvenient truth to the attention of decision-makers and to the world’s public. It is equally important that scientists understand the complexity of changes in the Arctic and what they may bring about. Without this detailed knowledge any strategy of mitigation or adaptation will all too easily fail.

From everything I have seen during my short stay, from the commitment, enthusiasm and hard work of everybody I have met here, I have no doubt that the CFL study will very substantially add to this knowledge. My week on board the Amundsen has certainly widened my own understanding of this fragile environment.

Many thanks to David Barber, Dan Leitch, the Canadian Coast Guard, all CFL scientists, and the amazing Amundsen crew, for having made this possible.

Quirin Schiermeier

Posted by Quirin Schiermeier at 08:14 PM | Permalink

Spending time on board a research ship inevitably blurs the separation line between reporting and doing science, even though most of the time the 'science' part of it is limited to dragging a sled-load of gear out onto the ice or, at best, pulling up a sampling net from a dive hole.

But today I have perhaps contributed to science a little bit more than usual, if only by passing on information. Yesterday evening I handed Dave Barber, the chief scientist of the Circumpolar Flaw Lead study, a paper coming out on Friday in the journal Geophysical Research Letters (which my ever-alert colleagues had sent me). The paper describes how, in a model, Arctic sea ice loss leads to strongly accelerated permafrost thawing on land. Dave promised he would read it.

When I entered his office this morning, he was brimming with enthusiasm. "Very interesting stuff," he said. "We should really start looking for what's going on in the Canadian permafrost. A model study like this could direct an observational study. Actually, I think I'd like to do this myself."

The paper, written by a team led by David Lawrence of the National Center for Atmospheric Research (NCAR) in Boulder, Colorado, suggests that if massive sea ice loss, such as occurred last summer, will happen ever more often, Arctic land warming could triple in the near future. This would have an effect on the rate of permafrost melting up to 1,500 kilometres inland on the continents surrounding the Arctic Ocean.

Thawing permafrost can destabilize houses, warp roads, and buckle trees. As Arctic soils hold around one-third of all the carbon stored in soils worldwide, their thawing may also add substantially to the release of greenhouse gases into the atmosphere. As Lawrence emailed me: "If sea ice extent continues to retreat rapidly, then we can probably expect an increase in the rate of warming over land and that this increased rate is likely to contribute to some near-term permafrost degradation, especially where permafrost is currently warm and vulnerable."

In the last century, the Arctic has warmed by around 3.5 degrees Celsius. And since the 1980s, when the warming trend kicked into gear, the multi-year sea ice pack has decreased by more than 10% per decade. This is equivalent to some 70,000 square kilometres - the area of Lake Superior – per year.

But it was only last summer that scientists observed what many say was a catastrophic loss of ice in the Arctic Ocean. By September, when the ice is at its seasonal minimum, it had shrunk to some 4.3 million square kilometres – a reduction of 65% relative to the 1987-2003 average.

Throughout October to December last year, the CCGS Amundsen (the Canadian icebreaker I'm currently on) sailed in open waters in the eastern Beaufort Sea, a region that should normally freeze in fall. Unusually frequent and strong storms had once and again mixed the upper layer of the ocean, bringing warmer water to the surface and preventing it from freezing.

"Our observations are very much of line with this paper," says Barber. "We don't do terrestrial work, but from a sea ice view accelerated melting is certainly what we're seeing. Our data, and everything we experienced over this last year, agree with what the model study predicts might happen in the future."

He doesn't expect a recovery of any kind this year. Our current study areas, the Amundsen Gulf – the western gate to the Northwest passage - is mostly ice-free already, and the unusually sunny and warm weather during the last 10 days has added to the rapid melting of the remaining ice in the region.

The large patches of dark open ocean allow for increased absorption of sunlight, which at this time of year shines 24 hours a day. If there was more ice, the white surface would reflect back to the atmosphere a much larger portion of sunlight. This so-called ice-ocean albedo effect is the dominant of several climatic feedbacks in the Arctic. "The warming effects here have a tendency to accumulate, which is why we will likely see a repercussion of last year's event in 2008," says Barber.

"There's an awful lot of heat accumulating in the upper part of the sea," he adds. "It may take until late autumn before the ocean gets rid of this excess heat, and it's intuitively obvious that its horizontal transfer will heat the terrestrial environment."

Models such as as the Community Climate System Model used by Lawrence and his team capture many, but not all, feedbacks that contribute to Arctic warming. What the study does not account for, says Barber, is that the open ocean is a magnet for storms feeding on the released heat. Models can't usually represent storms because they happen on too small a scale. But although small-scale, storms add quite some complexity to the marine-terrestrial connection in that they mix the ocean, keeping it warmer than usual, and bring precipitation. More snowfall on land will insulate the ground from warm oceanic air and might help prevent soils from rapid thawing.

Posted on behalf of Quirin Schiermeier

Posted by Alex Witze at 02:39 PM | Permalink | Comments (1) | TrackBacks (0)

From the editors: We've posted a Flickr set of some images Quirin (yep, that's him in this photo) took aboard the Amundsen, available here.

Posted by Alex Witze at 12:51 PM | Permalink

I cornered Harvard’s George Daley shortly after this afternoon’s opening symposium at the International Society for Stem Cell Research meeting in Philadelphia, and asked him for some stats and trends at the meeting. He’s the current president of ISSCR. There are 24,000 2,400 pre-registered attendees, he told me. That’s only 24 2.4 times the size of the last meeting I attended. As for trends: “There’s certainly a bit of Shinya-mania,” Daley said. He was referring to the focus on induced pluripotent stem cells (iPS cells), adult human cells reprogrammed to a stem cell-like state thanks to a couple of transcription factors by a Japanese group led by Shinya Yamanaka.

**Note updated numbers. It was a big meeting, but not that big! 24,000 would be getting into society for neuroscience range!

Daley wasn’t kidding. Cruising the poster session this evening, I was intrigued by the dense clump of bodies congregating around a handful of posters in one corner of the exhibit hall. All of them had to do with using variations on the so-called “Yamanaka factors.” Yamanaka used four, but there was a poster talking about using just two (Oct4 and Klf4) on adult neural stem cells with high efficiency. The work, presented by Vania Broccoli of San Raffaele Scientific Institute was drawing a crowd. Next to him Mali Prashant of Johns Hopkins was presenting data on reprogramming using non-integrating lentiviral vectors. John Dimos from Harvard was presenting work on developing models of the neurodegenerative diseases spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS) respectively in embryonic stem cells (retrieved from discarded embryos that had been diagnosed as carrying SMA associated mutations), and – you guessed it – induced pluripotent stem cells derived from the cells of adults with ALS. According to the poster, the SMA cells have a distinct phenotype with low numbers of motor neurons compared to other ES cell cultures that can be rescued genetically. The ALS cells are still being worked on. Dimos' PI, Kevin Eggan, has been trying to do the same work modeling ALS through stem cell cloning, essentially dropping a nucleus into an egg and deriving embryonic stem cells from the resulting embryo. But eggs have been scarce.

Posted by Brendan Maher at 04:55 AM | Permalink

After five days of shaking, TEGA will finally get around to some baking. Last Friday, the robotic arm dropped some soil onto the screen door of one of the ovens for TEGA, Phoenix's main chemical analysis instrument. But the soil was apparently too clumpy. Mission scientists sent commands to vibrate the instrument, which resulted in some material getting through the screen (see the animated gif here). But somehow it wasn't getting into the oven. Today, something finally gave -- was it the weather? was it the vibrating? -- and the oven is now full. Now they've got to worry about contamination.
For future TEGA tests, the team is experimenting with a new “sprinkle” test. Instead of burying the TEGA door in one big dump, the team may angle the scoop, and then run the ice rasp at its back – vibrating the scoop enough to send a fine stream of soil particles over the edge.

Posted by Eric Hand at 10:39 PM | Permalink

Harvard’s Doug Melton, in a plenary talk this afternoon to open the International Society for Stem Cell Research (ISSCR) meeting in Philadelphia, actually didn’t talk about stem cells at all. Rather he discussed new results showing direct differentiation of pancreatic tissue into the elusive and important Beta cells, skipping stem cells altogether.
It was clear from the opening session, that a large part of the conference would focus not on the derivation of stem cells, but rather their re-differentation into useful tissues, which is not so easy as one might think. Take the beta cell for example. Melton has had a long-standing project to derive beta cells from es cells. The potential is obvious. For folks with type 1 diabetes, beta cells can be transplanted with limited success, but are currently in short supply (cells from two cadavers are required for the so-called Edmonton protocol).
After four years of work trying to use chemical compounds to edge stem cells down the developmental path of the insulin producing beta cells, he found two with 70% efficiency in moving the cells the very first step in a process that looks to contain maybe six. So, his group began experiments to short circuit the process. Rather than taking an undifferentiated stem cell, could one take a fully developed adult cell and switch its fate using transcription factors without reverting to stem cells? The answer, ostensibly seems to be yes. Screening for upwards of 1000 factors in 5000 mouse embryonic tissue samples, Melton’s lab identified 28 factors that appeared closely related to beta cell differentiation formation. Paring down brought the number to nine. Using a virus to inject the genes that encode these transcription factors into the pancreas of living mice, they were able to cause exocrine cells in the pancreas to start producing insulin and look just like beta cells in every way they’ve looked. Melton says, it’s “not the case that they’ve just turned on the insulin genes. There’s a panoply of genes turned on and off in response to these transcription factors.” They even started producing VEGF and promoting angiogenesis to get blood supply. The group has been able to reliably convert cells to insulin producing beta cells using just three of the nine genes: Ngn3, Pdx1, and Mafa. Mice in which islets had been chemically ablated achieved some level of blood sugar control, but not that of wild type. And despite waning expression of the three genes they injected, the phenotype of the transformed cells remained for several months. Melton says he wouldn’t necessarily predict a gene therapy approach based on his findings, but if in vitro technologies could be adapted, they might increase the number of beta cells for transplant operations. This type of cellular reprogramming involved here is fascinating. I remember when few believed de-differentiation from adult cells to pluripotent stem cells was possible with out the help of egg cytoplasm. iPS cells proved that wrong. This fate-jumping reprogramming without intervening de-differentiation is even more astonishing.

Posted by Brendan Maher at 09:34 PM | Permalink

Having spent almost five hours out on the ice yesterday, I feel dog-tired today. People here are telling me that this is normal. (No, it was not a bar night yesterday).

In the wee hours of the morning we left Darnley Bay, where we had stayed put for the last couple of days, and set out into the Amundsen Gulf. Today is an open water day, with lots of sampling activity going on on deck, for nutrients, contaminants, seafloor sediments, plankton - the whole range. My cabin mate Mukesh, who’s never been in a boat on the ocean before, is getting bounced around on a zodiac they have just put at sea to do some optical profiles and deploy a drifting meteorological buoy. And the poor boy gets so easily seasick …

Here’s a picture of Dave Barber, our always busy chief scientist.

The sky is still perfectly blue, but a fresh easterly breeze is blowing, and the waves are not that small. The Amundsen is gently rolling and steaming, amplifying my tiredness and the sensation of dilated time. I have only been on board for six days now, but it feels like I’ve been seafaring for weeks.

This feeling of being astray in the otherwhere of the world ... I guess at heart I am a romantic.

A number of visual artists and composers have been, or will still come, on board the Amundsen to try to evoke through their art the essence and mood of the Arctic. David Scott, a composer with the Manitoba Chamber Orchestra, is in the process of writing a musical piece based on impressions he gathered during his stay in spring. Another Canadian composer, Vincent Ho, will come on board during the next leg of the CFL study. He plans to write a piece for the Winnipeg Symphony Orchestra, which will be performed during the Winnipeg new music festival in February 2010.

Together with his brother Doug, a retired professional photographer, Dave will also produce a coffee table book about the CFL. He showed some slides yesterday as a foretaste.

Dave is always keen to point out that one of the intentions of the CFL study is to merge western scientific knowledge with the aboriginal tradition of knowledge. In fact, the traditional knowledge team, which carries out surveys among the Inuit and other people living in the Arctic, is the largest of the ten CFL project teams.

In summer, a group of Inuit pupils will spend some time on board the Amundsen to team up with the scientists and take science classes, from meteorology to marine biology. I bet they will like it a lot.

Quirin Schiermeier

Posted by Quirin Schiermeier at 01:17 AM | Permalink

“The scatterometer is purring like a kitten“, Randy Scharien proudly told the sea ice team when we came back from the ice today, just in time for lunch (Tuna Salad, Italian Sausages with Rosée Sauce, Queen Elizabeth Cake – have I mentioned that Jacques Beaudet, our chef cook from Shawinigan, Québec, is a true wizard?)

Randy, Mukesh and I had set out onto the ice after breakfast to troubleshoot the radar scatterometer, which is supposed to take time series of the physical surface properties of the sea ice.

The generator-driven machine had stopped runing at some point early in the morning. I rolled my eyes when I saw the complicated set-up. But Randy hooked up a keyboard to the console that controls the radar, hit a few keys, and got the radar running again in less than a minute. “Just a software glitch,” he said. “No big deal, fortunately."

At a spot nearby, Mukesh has installed a prototype laser device with which he measures surface roughness over a melt pond (as an indicator for turbulence at the air-water interface). Besides being awfully skilled mechanics, computer programmers and mathematicians, Mukesh and Randy remote sensing experts. The reason why they are interested in the physical properties of ice and melt water - their electrical conductivity, resistance, and permeability to microwaves – is because this information helps the interprete and calibrate satellite data, such as images from NASA’s ICESAT and Canada’s Radarsat missions.

Satellite sensors cannot easily distinguish different surface features of the frozen ocean – ice, melt ponds, and the transition zones between the two - which all have very different properties, for example in terms of how they reflect the incoming sunlight. ‘Ground-truthing’, as scientists call it, is therefore necessary for getting the best out of satellite data, and ultimately for improving the predictive skills of sea ice models.

A note:

The daily sampling, data collection, repair work, and what not, is being done regardless of weather and light conditions. Right now it is bright and unusually warm , so warm actually that one doesn’t even need to wear gloves outside.

But this is exceptional. At more extreme temperatures, turning knobs, using laptop computers, untying knots, twisting a piece of wire, or just taking notes, gets very challenging. Just bear in mind that during most of the Arctic winter one cannot work without gloves on for more than a few seconds without risking serious frostbite. This aspect of polar research is not always appreciated.

Quirin Schiermeier

Posted by Quirin Schiermeier at 04:50 AM | Permalink

June 8, 2008

Perfectly clear skies, for the sixth day in a row now. Dave says that in he has never experienced such an extended period of sunny weather in the Arctic in 25 years.

Being exposed to intense sunlight 24 hours a day the ice just keeps melting away. We’re six weeks or so ahead of where we should normally be, in terms of climatology, says Dave.

We do have found a spot in Barnsley Bay where the ice has not yet broken up, but the melting ponds are getting larger and large. Some ponds have started to drain through the ice column, which weakens the ice even more.

Anyways, I went out onto the ice for the firts time today. I helped a team collecting water samples from a hole they had yesterday drilled in the one or so metre-thick ice.

Leaving the ship by the gangway, wearing heavy rubber boots and the obligatory red Mustang suit, was a strange sensation. From afar, the mighty red hulk firmly locked in the ice is a majestic view. The morning air was fresh and not too cold, the silence overwhelming. Brent carried the gun that is mandatory for team’s heading out to the ice,. We didn’t encounter a bear, though, only a seal popped up its little head somewhere near.

The hole is in half a kilometre’s distance from the ship. We put all necessary stuff – canisters, hoses, some bars and a rather heavy battery – in two large plastic sleds which we dragged without too much effort across the ice and through the numerous melting ponds along the way. The greenish icy water through which we waded looked treacherous, but proved knee-deep at best.

While we recovered the water samples, from two metres and seven metres depth, the diving team that had set out with us began pitching a tent for the scuba divers which are supposed to start their programme in the afternoon. In the distance, small groups of red-clad scientists were busy deploying and reading all kinds of exotic instruments.

But there’s not much time left for doing exciting things on the ice, at least not in the area around here. We will likely stay here until Monday, and then steam to a mooring station in the Amundsen Gulf to do sampling work in open waters. Later in the week, Dave plans (but plans can change quickly here) to sail on into the fast-ice on the northern side of the Gulf, where the latest satellite images suggest that the ice is still more stable.

Quirin Schiermeier

Posted by Quirin Schiermeier at 02:45 AM | Permalink

June 7, 2008

“On an expedition like this there’s always a plan A, B, C for what to do,” chief scientist Dave Barber said at the science meeting yesterday. These little meetings are being held every evening in the officer’s lounge to dicuss plans for the next days, lab time allocation, the ship’s course, and the like. “But sometimes you need to go along with plan I, J or K, ” he added, reminding everybody that field work in the Arctic doesn’t always go smoothly.

What had happened? Well, the condition of the ice had pretty much spoiled yesterday’s programme. When at around 7 pm we got to the spot of a former ice camp where a number of instruments had been deployed just three days ago, and where the teams (and I) were supposed to set out onto the ice to collect data and install new instruments, we saw that the ice had since broken in slabs separated by gurgling water. The only instrument still in sight was a meteorological measurement tower drifting on an ice floe, precariously close to a large pool of open water. This was not the spot where you would like to walk out onto the ice.

Dave had the skippy boat put to sea to recover the station. In the meantime, the helicopter hasd set ut in search of the other missing equipment. It turned out that most of the stuff, sediment traps and the like, had drifted some two and a half miles west. Everything was eventually found and recovered.

At first I was a little disappointed that I had to stay on board. But well, the little rescue episode, helicopter and all, seemed also quite dramatic. (Be assured that not even on an icebreaker exciting things happen every hour. The first thing really you have to learn here is that you’ve always got to wait) .

But then Dave said that such things happen all the time. The really remarkable thing about it was that all equipent was recovered. Normally, when the ice breaks up, pieces of equipment will just fall into the ocean and get lost.

Now, the problem is that the ice edge has become really quite weak. The strong wind in the last few days has sufficed to break up the ice in some areas.

What will happen next is not yet quite clear. The ship will likely have to relocate several times in the next days and weeks to find spots where instruments can be installed. We’re now supposed to steam to Darnley Bay, just east of Franklin Bay, and try our luck there. If the ice everywhere in the region turns out to have become too thin we might not be back in the ice at all, doing other things in open water instead. There’s quite a lot of action going on on the bridge right now. But as Dave said, whatever happens, there’s always a plan X available.

Quirin Schiermeier

Posted by Quirin Schiermeier at 12:11 AM | Permalink

June 6, 2008

A perfect sunny day again. There was no night, no darkness, not even a dawn. With bright daylight lasting for 24 hours, time seems to stand still. Meals and other little rituals that structure a day gain a new significance when the sun never sets.

A few observations:

Arctic exploration is no longer the male business it used to be. At least half of the partcipants in this leg of the CFL study are female scientists, mostly PhD students and postdocs. The ship is also commanded by a woman, Captain Lise Marchand.

In trems of safety and comfort, the expedition has little in common with what 19th century explorers must have risked and endured when setting out towards the poles. The Amundsen is no luxury liner, but life on board is just as enjoyable as as would be a stay in a hostel for the dedicated young outdoor lover. With the nearest store a 60-minute flight away, we are still pretty isolated out here. One young scientist who has been on board for 16 weeks now told me this morning that the Kiwi she had for breakfast (from the fresh supplies delivered yesterday) was the first fruit she had eaten in three weeks.

The morning was dedicated to ‘familiarization’ with the safety and security rules. We went on the life boat, tried on life jackets, learned what to do and where to gather in case of an emergency, and so on. A brief medical examination, too. In the afternoon there was an alarm exercise.

After lunch the ship has started to move. Just minutes later we reached the ice edge and continued in open water. We are now steaming to a near-by spot in the ice where ice sampling tools and other equipment are to be deployed. I will join one of the teams who will go out onto the ice. Mukesh, my cabin mate who studies the physical properties of sea ice, has been fiddling around all day with a laser profiler he is meant to install in the evening. Our cabin looks like an electronics workshop.

There is less sea ice in the Amundsen Gulf than one would typically expect at this time of year. At which point the remaining land-fast ice – the ice attached to the coastline - will start to break up nobody kows. Dave Barber says it may happen next week, but that it could just as well be next months. In any case, everybody here whose scientific work involves ice is trying to get it done as long as the ice is still there.

The ice along coastlines, and the permanent ice pack covering the central part of the Arctic Ocean, have been shrinking in recent years. What causes the dramatic retreat is not exactly known. It seems to be driven by climate warming, which is more pronounced in the Arctic than in most other parts of the world. Changes in atmospheric circulation may also play a role. But whatever the physical causes may be, shrinking and thinning sea ice will affect Arctic people and ecosystems alike. One of the purposes of this trip is to find out how.

Quirin Schiermeier

Posted by Quirin Schiermeier at 03:03 AM | Permalink

Is Phoenix, and one of its premier instruments, TEGA, covered in too much microscopic crud from Earth to detect Martian organics? That's the question I try to explore in my latest story on the main Nature news site. TEGA, pictured on the right, is about to begin baking soil samples and sniffing the gases that come off it in the hopes of detecting organic molecules. But whether the TEGA team can say anything definitive will depend on how free the instrument is of Earth organics. Yesterday, Phoenix had its scoop poised at the edge of one of TEGA's eight oven doors, and today, it was going to let the soil dribble through TEGA's sieve.
New Scientist reporter (and former Nature intern) Ewen Callaway has an excellent story on a related issue: Are Earth microbes so hardy that they could survive on Mars? A JPL microbiologist found a lot more bugs than you might think living in supposedly clean assembly rooms. And while great care was taken with the robotic arm, wrapping it in a biological barrier, there are other parts of the spacecraft that were not kept as clean. What about the lander feet? They don't interact with the soil as much as the robotic arm, but they could easily have landed directly on ice. Is an antiseptic wipe down before launch enough?

Posted by Eric Hand at 08:06 PM | Permalink

June 5, 2008

After an epic journey, on four planes and one helicopter, I have at last arrived on board the CCGS Amundsen.

The final leg of my trip, the short transfer from Inuvik to Cape Parry at the northern tip of Canada’s Northwest Territories, was easily the most spectacular flight of my whole life. The tiny aircraft flew at very low altitude, so that every barren hill and every glittering lake in the tundra below seemed almost seizable. Then we were out on the frozen Franklin Bay, an inlet of the Amundsen Gulf, and headed towards the edge of the fast ice. We went down on a gravel airstrip next to an abandoned cold-war early warning station. From there a helicopter took us on board the icebreaker which is currently staying put in the fast ice at only a few ship lengths distance to the ice edge.

I was not the only person to get on board today. It was in fact a full crew change for Leg 9 of the Circumpolar Flaw Lead Study, currently the largest project in the International Polar Year research programme. Some 80 crew members and scientists were replaced – a logistical masterpiece.

First thing we did upon arrival on the ship was carrying down from the landing platform to the main deck the immense amount of cargo - personal luggage, scientific equipment, food - which the helicopters had also delivered. What remained of the afternoon was dedicated to getting familiar with the ship and with life on board. After dinner the newcomers met in the small conference room for a first get-together with captain Lise Merchand and chief scientist Dave Barber.

Even so, many things are still a bit confusing to me (I'm a landlubber, really). About some of the exciting science that’s being done here I will report throughout the next seven days. But one thing I do already know: It is a great privilege to be guest here, and to be able to report from a spot most people, science reporters included, never get to see.

It was in Winnipeg in the very early morning today, when sitting around in a hangar and waiting for the charter plane to arrive that would take us to Inuvik, that I began to realize that I was embarked on a real adventure. The feeling of excitement lingers on as I’m now sitting in a cabin I share with a PhD student from India who just went to sleep. The ship engines gently roar, but we’re not moving. Looking through the porthole I see a seascape depicting grandiose white nothingness bathed in the mild light of the midnight sun. It is an eerie yet transcendent view, acknowledging as it does the silent glory of nature and the frailty of our wishes.

Quirin Schiermeier

Posted by Quirin Schiermeier at 05:31 AM | Permalink

Yesterday, Mars Odyssey failed to send Phoenix instructions for the day -- and so engineers have switched back to Mars Reconnaissance Orbiter as the go-to relay link.
This is the second time that Phoenix has lost a day due to a balky communications link. When it happens, Phoenix still stays reasonably busy, following "run-out" instructions that tell it to take panoramic pictures. But it isn' t what the scientists want to be doing. Yestersol (sorry, hooked on the term), Phoenix was supposed to move its first soil sample to the edge of TEGA's maw. That's going to happen today, assuming the MRO uplink works. Tomorrow Phoenix will tilt the scoop and drop the soil in. And so on, day by day.
The team is prepared for the slow work -- even budgeting for down days like yestersol. JPL flight systems engineer Chris Lewicki says that the team should accomplish all its science goals even if 30 of the mission's 90 days are lost to the unforseen.
The press conference focused on some of the first optical microscope pictures in MECA. Some really cool images of three grains, likely kicked up during the landing, can be found here. MECA lead scientist Michael Hecht said these pictures had 10 times better resolution than microscopic pictures from the Mars rovers. That's a nice superlative: The tiniest things ever seen on Mars.

Posted by Eric Hand at 08:22 PM | Permalink

Also in this week's Nature, we did something unusual: a "snapshot feature." Some of our editors were so taken by the photo of Phoenix descending in front of Heimdall crater that they carved out two full pages in our features section, usually reserved for longer, analytical stories.
If there's ever a time to pilfer the copy of Nature from the departmental common room, then this week is it. Heck, I'd pay money for a nice glossy poster. The folks at Mars Reconnaissance Orbiter should seriously start selling prints of this -- maybe they can pay for the cost overruns on Mars Science Laboratory.

Posted by Eric Hand at 03:47 PM | Permalink

I have a new story up on the main Nature News site about the mystery of the polygons on Mars, which are analogous to the polygons found in the Arctic and Antarctic on Earth. Mike Mellon thought he had them all figured out -- he had a model that perfectly explained the five meter polygons he was seeing from Mars Reconnaissance Orbiter's HiRise camera (pictured here). Then Phoenix landed and they were too small. Strangely, Mellon also sees the faint imprint of really large polygons, maybe more than 20 meters across. One idea is that each polygon size reflects the freezing mechanics of a different climatic epoch. The most prominent polygons reflect the active climate, while the receding ones are the half-erased remnants of climates of yestersol (a Mars-mad neologism that I heard a JPL engineer use yesterday). The surface of Mars would therefore be a palimpsest (perhaps my favorite word in the English language).

Posted by Eric Hand at 02:49 PM | Permalink

I’ve snuck into a quiet little room with big comfortable chairs and more than one sleeping microbiologist. (With ‘sunrise sessions’ starting at 6.30 AM, who can blame them!) So, as I listen to the gentle snoring of one of my companions, here are a few highlights from a press conference on the human microbiome.

As a loyal NatureNews reader, you’ve heard plenty about the microbiome (for instance here or here). Basically it’s the sum of all the bacteria living in the human body. A frequently trotted out statistic: there are ten times more bacterial cells in the human body than human cells. It’s incredibly complex. Many of your bacteria are different from my bacteria. And the population of bacteria on your forearm is very different from the population in the crease of your elbow, said NYU’s Martin Blaser. David Relman of Stanford noted that our microbiomes might one day be used as a biometric, like a fingerprint, except that the microbes might reveal a bit more: where you’ve been, what you ate while you were there, etc. He also pointed out that microbiomics (my word, not his) began in 1683 when van Leeuwenhoek scraped one of his teeth and compared the results under a microscope to samples taken from his colleagues.

The panelists agreed that since we don’t understand everything that our microbes are doing for us, we also don’t understand the long-term ramifications of taking antibiotics. Blaser speculated that there could be cumulative effects from disrupting your microbiome that we don’t yet appreciate. Claire Fraser-Liggett said her friends call her a 'thereapeutic nihilist' because she avoids taking antibiotics whenever possible.

Blaser made another interesting comment: that our current focus on finding genetic variations linked to disease may one day give way to a realization that differences in our bacteria are just as important.

Posted by Heidi Ledford at 07:26 PM | Permalink

No, that isn’t Phoenix PI Peter Smith. And that’s not the Surface Stereo Imager.
That's a decade old picture of David Paige, PI for the doomed Mars Polar Lander, with the previous incarnation of the SSI.
On one of the recent Phoenix conference calls, a journalist asked -- had anyone talked to Paige? Did he watch the landing? Good questions. I called him up -- he’s a professor at the University of California at Los Angeles -- and had a quick chat. Turns out he did watch the Phoenix landing from JPL, with his 5-year-old son.
First, the background. Mars Polar Lander was headed to the south pole to perform a similar mission as Phoenix, but was lost upon entry to the atmosphere in 1999. Its failure led to the cancellation and closeting of the parts that were going into the Mars Surveyor lander -- and it was those parts that were resurrected to make Phoenix.
Paige recalled the tense moments of his landing operation, which also occurred at JPL. It was a low budget operation, and Polar Lander didn’t have direct telemetry to Earth during its descent. From the time it left the cruise stage, until it touched down and started beaming signals back to Earth 20 minutes later, mission managers had to wait in silence.
Paige recalled the silence persisting after 20 minutes. And persisting. That began weeks of fruitless searches for any signal that Polar Lander was alive. Its wreckage (though it might not have crashed) still hasn’t been found. Instead of seven minutes of terror, Paige had months of anxiety, followed by years of disappointment. “We’ll get closure eventually,” he says. “It’s like the lost relative that went on the hiking trip and never came back. And you never found the body.”
“We came very, very close to doing something unique. You can’t help but wonder what we might have discovered…” he says, trailing off.
But he’s not feeling bitter by the success of Phoenix. Bittersweet, maybe. It brings back difficult memories, but he’s not jealous. “They deserve success and so far it looks like they’re getting it.”
He also puts a positive spin on the failure of Polar Lander, saying it was necessary in order for Phoenix to succeed. The Phoenix team scoured the old Surveyor parts relentlessly, and identified and eliminated failure modes.
After several months of searching for Polar Lander, Paige sent an email to his team, saying it was time to call off the mission. Paige didn’t drop off the face of the Earth, but he did decide not to get involved with Phoenix. Five years down the drain was a lot, but not his whole career. He’s now a PI for a thermal mapping instrument on the upcoming Lunar Reconnaissance Orbiter. “There are always more chances. It’s not the end of the world,” he says. “No mission is the last mission to Mars.

Posted by Eric Hand at 03:54 PM | Permalink

Proof that life can survive on Mars.

Posted by Eric Hand at 08:17 PM | Permalink

Richard Henkel of the Centers for Disease Control gave a talk yesterday about biosafety in the lab. It was primarily a nitty-gritty run-down of which forms to fill out if there’s a theft, loss, or release of potentially harmful microbes or toxins that are on the US ‘select agent’ list. In case you’re wondering, you may need to file a 'Form 3' in that event. And he gave a few interesting statistics on how many Form 3’s have been filed over the years:
2003: 4
2004: 19
2005: 19
2006: 24
2007: 60 (plus one case in which an institution failed to report an illness contracted from on-the-job exposure)
2008 (through April): 32
(Henkel attributes the dramatic increase to higher awareness of proper reporting.)

Posted by Heidi Ledford at 06:53 PM | Permalink

Between the talks and the poster presentations, researchers here have been studying microbes in just about every environment you can imagine. Here’s a quick run down of what microbes call home: the crook of your elbow, 26,500 year old Antarctic algal mats, the space shuttle assembly platform, a tar pond, hospital room drains, stored space shuttle food waste, the guts of the medicinal leech Hirudo verbana, ready-to-use fresh salad in Vienna, infant formula production facilities, Chihuahua cheese, uranium contaminated groundwater, sea turtle tumours, the ‘dead zone’ off the coast of Oregon, and of course the usual deep sea thermal vents and acid mine drainage pools.

Where they do not call home: the Atacama Desert.

Posted by Heidi Ledford at 06:22 PM | Permalink

Nature reporter Quirin Schiermeier is spending June 5-12 aboard the Canadian research icebreaker CCGS Amundsen, as part of a project to study climate change in the high Canadian Arctic.

The Circumpolar Flaw Lead System Study, led by David Barber of the University of Manitoba, is one of the largest projects in the International Polar Year research programme. During the field season, from October 2007 to August 2008, more than 200 scientists from 15 countries will be studying the impact of climate change on sea ice, Arctic peoples, and marine ecosystems in some of the biologically most productive areas of the Arctic.

Quirin will board the Amundsen in Inuvik, in Canada's Northwest Territories, as the crew changes over for Leg 9 of the expedition. You can read his trip diary on the Nature newsblog here; more about the Amundsen icebreaker here; and more about the Circumpolar Flaw Lead study here.

Image: Arctic Ocean Sciences Board

Posted by Alex Witze at 05:21 PM | Permalink

Phoenix's robotic arm has scooped up its first mouthful of Martian soil, mission scientists announced today. In a test "dig and dump" area to the west of the "National Parks" that are off limits for now, the robotic arm easily slid into the soil. The color picture here, taken with the LEDs of the robotic arm camera, gives a good sense of the crumbly, crusty overburden that the team will be digging through to get to the ice that they're pretty sure lurks just below.
In fact, they might have reached it already. If you look really carefully at the picture, a quarter of the way from the right, you can see what appears to be filigrees of frost. Robotic arm lead Ray Arvidson, of Washington University in St. Louis, said the white stuff could also be a water-borne magnesium sulfate salt.
In other news, PI Peter Smith said that a back up filament -- used to ionize the gases coming off baked soil samples -- should work as well as the primary filament, which is suffering from an electrical short circuit. Smith said the team plans to dump their first soil samples into the one of the ovens either tomorrow or the next day.
Image: NASA/JPL/University of Arizona

Posted by Eric Hand at 09:58 PM | Permalink

Two researchers from the University of Colorado in Denver, Munira Albuthi and Timberley Roane, are proposing an unusual use for an unusual bacterium: detoxifying Native American artifacts.

The bacterium is Cupriavidus metallidurans CH34 (the bacterium formerly known as Ralstonia metallidurans CH34, for those of you keeping track). C. metallidurans has an unusual ability to flourish around heavy metals at concentrations that would normally be lethal. (The critter was first isolated from the sludge of a Belgium zinc decantation tank, according to the Joint Genomes Institute.)

Now, Albuthi and Roane hope to use the bacterium to decontaminate Native American artifacts. The artifacts were once collected by museums, but have since been returned to Native American tribes. Unfortunately, before they were returned, the artifacts were treated with a mercury-containing pesticide for preservation. The mercury poses a health hazard, and Albuthi and Roane hope to spray down the artifacts with C. metallidurans, which is able to detoxify the mercury. So far, they’re just in preliminary stages of testing, but the bacterium was able to remove 60% of the mercury from a mercury-soaked piece of paper.

Posted by Heidi Ledford at 07:14 PM | Permalink

Here’s one of the more creative uses of viruses that I’ve come across: harnessing viruses that attack bacteria to kill off a bug commonly associated with particularly nasty pimples.

The bacterium in the crosshairs is Propionibacterium acnes, and has been linked to the more serious pimples of the most common form of acne: “acne vulgaris”. Michael Davis of Central Connecticut State University has been swabbing the foreheads, noses, and backs of students to build a collection nearly 400 P. acnes isolates. He and his team of graduate and undergraduate students then tested several dozen viruses against the P. acnes cultures. They’ve found a few that can kill specific strains of P. acnes, and now they’re exposing their viruses to UV light to create viral mutants that, they hope, will be active against a wide variety of P. acnes strains. Davis along with his team (undergrads Margaret Zurowski and Brandon Albright, and grad student Kathryn Neely) presented their work as a poster this morning.

Posted by Heidi Ledford at 07:04 PM | Permalink | Comments (2) | TrackBacks (0)

Hello and welcome to the American Society for Microbiology’s annual microbial extravaganza! This year’s shindig is in Boston, and the Boston Convention and Exhibition Center has literally laid out a red carpet to welcome the glitterati of the microbiology world. (I was amused to see that they’ve also placed the pressroom right next to the children’s daycare center. A subtle comment on our maturity level? Perhaps.)

Judging from this morning’s poster session, this looks to be a fun meeting. It’s a busy one, too – with over 3000 presentations, it can be hard to pick out which ones to attend. If any of you out there have suggestions to help me weed through the 300+ page program, please let me know: you can contact me by posting a comment here or via email: h.ledford at boston dot nature dot com.

Posted by Heidi Ledford at 06:35 PM | Permalink