Knoxville '82: Where Miscellany Thrive

Antarctica: Seal Wrangling: the Weddell Seal Research Team

vlicata — Thu, 14 Apr 2016 14:43:57 +0000

Antarctica: Seal Wrangling: the Weddell Seal Research Team

One of the cowboy science teams (or cowgirl science team – see photo) that I was able to spend some time with at McMurdo Station is the Weddell Seal Research Team under the direction of Dr. Jenn Burns of the University of Alaska. This multi-faceted science team spends virtually every single day during their field season tracking down tagged Weddell seals on the Ross Ice Shelf and performing a gigantic battery of physiological tests and measurements on them. Every day this group is either in helicopters (less frequently) or out on snow mobiles (more frequently) re-capturing animals that they already performed measurements on earlier in the season, in order to document their physiological changes throughout the reproductive season.

The picture below shows them in their lab space at McMurdo in a rare moment when they are all standing still. Jenn Burns, the project head, is on the left. The rest of the team shown here includes two grad students, a postdoc, two veterinarians, and a science-educator.

Jenn Burn’s project is looking at a variety of links between seal physiology and seal reproductive success. Different team members are looking at lipid levels, hormone levels, molt timing, timing of pup bearing (early or late summer), and impact of skipping a reproductive year, among many other variables that they are trying to link to reproductive success. It’s amazing how relatively little is known about Weddell seals. Regular pregnancy tests used in other mammals don’t work with the Weddell’s, so the team has implemented novel ultrasound procedures for determining if a seal is pregnant and for characterizing the developing fetus – which they also perform during the time that they work with each anesthetized seal out on the ice. Even significant aspects of the reproductive anatomy of the Weddell seals are relatively uncharacterized, and so some of that is also being documented by the team.

The precautions they take with the animals they study are quite intense: they have a permitting process that allows them to anesthetize and directly work with up to 24 seals on the ice during this window of the project, and a major role of the two veterinarians on the team is to make sure that the seal never goes into any type of distress and is successfully released after the team makes its measurements and takes their blood and small biopsy samples. The physiological samples are then processed for shipping back at their lab in McMurdo, and most of the detailed biochemical analyses will occur once the sample and the team are back in their regular lab at the University of Alaska.

As I have learned, Weddell seals are amazingly interesting animals. They aggregate in colonies, sometimes with hundreds in one colony, yet they stay relatively solitary within that colony. When they are “hauled out” and basking on the ice, each seal with be by itself with 1-2 yards or so between it and any other seal. In the water during the breeding season (mid December) the male Weddells keep and defend 3-dimensional territories – mostly linked to access points in the ice where seals can “haul out”. Females select routes through these male territories dependent on who they want to mate with. Females only give birth to one pup a season (apparently twinning in Weddells is far more rare than it is in humans). After they give birth to their pups they only care for them for approximately six weeks – after that the young seals are on their own. In the Ross Sea area right around McMurdo there are about 2000 Weddell seals that stay mostly in this region from year to year. One of the interesting inter-colony movement patterns that occurs during the breeding and nursing season is that the older (and wiser?) females will gradually move to areas around McMurdo where it is more reliably “easy” to haul out onto the ice during the season (some areas more consistently have thinner ice).

Although they will use natural cracks in the ice, the Weddells can also bore their own access holes with their teeth. They cut through the ice from below to make a hole, even shaping out somewhat of a ramp on one side of the hole where it is easier for them to haul themselves out with their front flippers. Since they have no land predators, the Weddells are quite patient and almost nonchalant about the researchers walking and working among them. Apparently other seals are not quite so chill regarding humans in their midst.

The day after day consistency and intensity of the work this team is doing is why I call them cowboy scientists – their unique combination of collecting “normal” animal data under rather extreme conditions miles out on the sea ice makes for some real adventure science.

vlicata Thu, 04/14/2016 - 10:43

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Ridley Scott Just Needs a Little Focus: A Review of the Martian

vlicata — Thu, 31 Mar 2016 14:10:10 +0000

Ridley Scott Just Needs a Little Focus: A Review of the Martian

The Martian is a feel-good, science positive, uplifting film about the power of the human spirit, botany, and engineering. It looked, from the credits, like it had at least 8 scientific advisors from NASA (and possibly other places). Too bad that Ridley Scott only half listened to them. As one of the primary sci-fi filmmakers working today, it’s kind of amazing how a lot of the science in Ridley Scott’s films sort of leaves a chalky taste in the mouth. (Take a look at this link for a scathing review of the science in Prometheus).

It’s clear that The Martian is science-positive – the main character’s facility with everything from chemistry to botany to electrical engineering is quite inspiring, even though, this itself it is one of the not-quite-realistic elements of the movie (I am told that the book does a better job of making Mark’s broad spectrum of practical knowledge believable rather than seeming almost savant-like as in the movie).

So, spoilers ahead, what’s good, what’s bad in The Martian:

Good:
1) A botanist as the hero! A scientist as the hero! And a plot that involves explaining what Mark was doing as he was doing it (although never far from the surface).
2) The whole problem solving aesthetic of the movie really captures the science and engineering spirit beautifully.
3) “I’m going to have to science the shit out of this” – what a great line!

Please don’t get me wrong – the Martian, on the whole, is one of the most science positive, science-career-inspiring movies to hit theaters in a long time – it is a step in the right direction – a big step in the right direction. But it’s only another step on a road that stretches out a bit farther into the future.

Sloppy Movie Science:
1) The hurricane force dust storm on Mars has already been acknowledged by the author of the book, and widely discussed, as a scientific inaccuracy “necessary” to the plot. This is, in my opinion, just a little bit lazy plotting and a desire for some dramatic visuals. There are many other possible reasons that Mark might have been left on Mars that are more realistic, but maybe less dramatic.
2) Making water from hydrazine. Hmm…hydrazine is rather toxic. Mark doesn’t wear any protective gear while working with it. He probably would have killed himself before getting much water, especially working with it as depicted in the movie.
3) The ship itself seems a bit on the absurdly large side – lots of long, apparently empty cylindrical corridors to fly through at high speed in microgravity – looks neat, doesn’t really match the reality of the ISS or any other ship ever yet sent into space. It even makes the USS Enterprise look cramped. Similar giant ship silliness has been pointed out for Prometheus.
4) Jessica Chastain as the commander of the mission? Couldn’t they get Zooey Deschanel? Or Sarah Jessica Parker? Could this be an embedded hilarious joke by the director? Apparently whoever cast the film was not allowed to meet any real astronauts. Jessica Chastain is a wonderful actress, she is just not the right actress for this part –she exudes little or no confidence, clarity, competence, intelligence, control or inherent leadership qualities of any kind. I don’t believe I would feel very safe on a ship in her command. Check out Anamaria Marinca in Europa Report if you want to see how one should cast this part. Check out any armed forces commercial on television if you want to see more appropriate portrayals.
5) I hypothesize that upon seeing astronauts scampering and scooting, and hopping along the outside of the space ship WITHOUT ANY TETHERS, that all 8 NASA advisors probably felt faint and secretly wondered if it was too late to take their name off the credits but still cash their checks. This is only a hypothesis, of course.
6) Is there really no other way to slow the ship down other than blowing parts of it up? Well, okay, none that involve awesome explosions in space (complete with sound! Just like in Star Wars, but unlike in 2001 A Space Odyssey, where accuracy was a bit more in evidence).
7) There might be an average 12-13 minute communication delay between Mars and Earth, but the much longer communication delays between “what Mark was doing” and “when the people on Earth figured out what he was doing” was kind of painful to watch, and underscored how fortunate it was that Mark seemed to be a cross between Einstein, Tesla, and George Washington Carver.
8) Like the dust storm that starts the movie, the whole rescue scene is way over the top, even beyond the lack of astronaut tethers (for everyone but Jessica, can’t lose her). This also has been discussed in a review in the Guardian.

It’s just weird that Ridley Scott, in a movie where accuracy actually makes more of a difference to the story, ignores enough science details to make an otherwise wonderful science movie become cringe-worthy every few minutes or so. I recently was working with a high school science teacher who said he had to walk out on the movie because the buildup of little mistakes became too great for him to tolerate. In general accuracy is more important in “near” sci-fi than in “far-in-the-future” sci-fi, and so matters more to the believability and integrity of the story in “The Martian” than in, for example, “Prometheus”. Maybe, but just maybe, with a little more attention to detail (i.e. maybe the level of detail one might have found if this were a movie about the French Revolution, for example), maybe “The Martian” wouldn’t have been nominated in the Best Musical or Comedy section of the Golden Globes. But this is only a hypothesis.

Despite all this grousing about details, The Martian is the most science positive blockbuster level movie from Hollywood in some time – and that alone is an important and significant accomplishment in my little opinion – just remember to squint through the parts that remind you of some of the answers you typically find on high school science tests – mostly well meaning, but not quite in tune with reality.

vlicata Thu, 03/31/2016 - 10:10

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I was more bothered by,

(a) how could he have an unlimited supply of Oxygen.
(b) The problem of radiation exposure without major protection.

The dust storm didn't seem that bad to me, it only had to threaten the return rocket, and allow debris to fly.

Of course as a guy who has had a long career in computing, hero #2 was the trajectories calculating kid*. Did he get fired for slipping the rescue possibility to the crew? But, sitting in the actual supercomputer? Looked great photographically, but even if the problem couldn't have be done on an average PC, he wouldn't need to be within several thousand miles of the actual compute server.

* Extra points for potential inspiration of African Americans thinking about STEM potential career path.

Replacing a blown hatch with duct tape re-enforced plastic film was also pretty egregious. Holding back .1 pounds per square inch would be unlikely, anything close to earth atmosphere would a at least a hundred times more pressure than that could possibly hold...

Reading the book would help. The problem being that the movie would be something like 5 hours long with lots of technical monologues to stay fully accurate. Oxygen is not a problem if you have plenty of energy - i.e. a solar array - and a machine for using that energy to split CO2.

It's a bit like the LOTR movies, which to me make very little sense without the books because so much is cut out of the movies - which makes you wonder how long the movies would have to be for completeness..

Antarctica: Cowboy Science

vlicata — Tue, 08 Mar 2016 16:03:15 +0000

Antarctica: Cowboy Science

Hi. Apologies for the radio gap. It turns out that Trish, the co-PI and irresistible force behind this project met with an immovable ice patch and broke her femur a few days ago at the Willy Field airport on the Ross Ice Shelf. She’s “fine” now, and freshly bionic-ized with new hardware pinning together her skeleton. Oh, and we got the shot, out at the airport, while her femur was still in two parts (a shot of one of the C-130 planes framed similarly to a Ponting photograph of the Terra Nova at dock).

Trish’s own experience underscores the originally intended topic of this particular post: cowboy science. Another of the striking elements of McMurdo is the sheer over-the-top physical intensity of the scientific fieldwork that is done here (and the scientists that do it). Many of the research support staff and researchers I met included people who guide climbers up mountains in their off-season time, or go to the 7am Insanity Workout sessions in the gym at McMurdo, before breakfast, or skate across the United States (complete with slides and short videos shown during a Monday night Travelogue in the Galley). These men and women are Antarctic cowboys in their own right, but many/most of them also use their special prowess to do their science as well: cowboy scientists.

Zach Sudman (in the picture below) works on the stream team. He lives and works in the Dry Valleys for the bulk of the summer season, climbing up and down hills and around lakes to make his measurements of the depth and flow of Dry Valley streams as part of the Long Term Ecological Research (LTER) project. The picture below shows him surveying a stream. This picture is posed similar to one of the many Herbert Ponting photographs of the initial surveying of Antarctica conducted during Scott’s expeditions in the early 1900's.

Zach’s colleague, Forrest (who is a mountain guide in the Antarctic off-season), said he hikes for many miles every day in the valleys, just for fun. He also collects water and algal samples as part of the LTER project.

Ian Barry, shown in the picture below this paragraph, spends the entire year in Antarctic, working about a mile and a half away from McMurdo at a site called Arrival Heights, where he is part of a research project that measures the temperature at the edge of space using laser detected shifts in the electronic state of iron atoms in the troposphere. Here he is on the roof holding a card over the emission tube for one of the lasers. This picture is posed similarly to a hundred year old Ponting picture of Nelson measuring the temperature under the ice on the Terra Nova.

Other cowboy scientists we met included a team that works on Mount Erebus (saw them around 3pm one afternoon leaving for a helicopter to fly up to the Erebus station, several thousand feet up the volcano, and they said they’d see us at the bar after dinner – no big deal, just gotta go up the volcano for a bit…). A team testing a new drill went up into the snow and ice field above McMurdo each day seeing how far their new drill would go (apparently no one knew how deep the snow and ice were there; they had gone down at least 1000 feet without hitting rock so far). Aneliya is a grad student who also works in the Dry Valleys, where she is part of a team that hauls about 100 pounds of lidar equipment up and over various hills to document the topological changes in various stream beds in the valleys. One afternoon she also hopped on a helicopter to fly out to Cape Royds and collect a water sample from Pony Lake – all in a day’s work for a cowboy/cowgirl scientist. David Ainely, who was mentioned in an earlier post helicopters around tracking the penguins – asking the helicopter pilots to land in various new places where he can then hike out of sight for an hour or so taking stock of where the penguins might have wandered.

Scientific field work anywhere is, of course, often challenging and difficult – the type of thing only people as obsessional as your average scientist will do – especially since the “payoff” is not financial, is not social, is not political, and is not measured in fame or celebrity – the payoff is the next data point. I often find it amazing how few of the “general public” really understand this about scientists – what we’ll do for the next data point. I also find it amazing how little filmmakers understand this about the scientists portrayed in their films, even with all the science advisors available to them. All science is adventure. Some of it, however - an hour helicopter flight out of McMurdo Antarctica and halfway across a frozen lake, or just below the rim of the Mount Erebus lava lake - is a little bit more wild west. Cowboy science.

vlicata Tue, 03/08/2016 - 11:03

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Antarctica: Links and Lack of Links

vlicata — Thu, 11 Feb 2016 21:30:17 +0000

Antarctica: Links and Lack of Links

Internet Links and Social Links at McMurdo Station, Antarctica.

Here are some links of interest related to Trish Suchy and my NSF Antarctic Artists and Writers Project:

Trish Suchy’s blog about our Artist’s and Writer’s project.

David Ainley’s website about his research on Adelie penguins: Penguin Science

The weather in McMurdo is here.

Zach Sudman’s blog (who we photographed in the Dry Valleys):

And here is the blog of Shaun O’Boyle, one of the Artists & Writers who was in McMurdo immediately before we were. He was/is doing a beautiful black and white photography project on McMurdo.

One of the unusual aspects of McMurdo social interaction is the apparent significant lack of linkage to the outside world. Everyone talks about what’s going on here, but rarely do you hear much about anything going on in the US or the outside world in general. Even on Superbowl Sunday, there were a few (and I mean a few) people who talked about the game – but far fewer than in the outside world (all day I heard only 3 unsolicited mentions of the Superbowl). Almost no one mentioned the Iowa Caucus. People rarely talk about their family or friends in the outside world. The feeling is similar to what I might imagine living in a space outpost might be like, at least as such is often portrayed in SciFi. What matters is here. It’s not that the outside world doesn’t matter, it’s just so far away and there is little anyone can do about it here. It’s a perfect place to escape the outside world and really feel like you are living in a remote and isolated colony. On some days I feel like we could be in a Buddhist monastery that happens to do science.

This apparent focus on the here and now probably is also somehow related to the extraordinarily high level of friendliness and cooperation here – a feeling of insularity and the interdependence and self-reliance needed to keep things working. If you have a problem, you need to rely on someone here and near, someone you eat breakfast, lunch, and dinner with in the same large room every day. The important links, needed to just get your work done and at times possibly live-saving, are internal not external. Perhaps this somehow conditions the brain to focus more energy on those internal links and to allow the external links to drift into the background. Although others here, including Trish, have also noted both the extreme friendliness and the lack of outside world discussions here, it is definitely possible that these “observations” are partly peculiarities of our own perceptions or the particular subsection of the town population that we hang out with. Certainly the friendly, “let me help you” attitude is an amazingly positive aspect of McMurdo – without which it would be difficult to get your work started or finished here. The apparent lowered outside world consciousness is neither good nor bad. It just is.

PS: Just an interesting update: one of the few "outside world" conversations I had was just after I posted this entry: someone saw my LSU shirt and asked me if I had heard about LIGO's announcement documenting gravitational waves. Since Joe Giaime (who is the Observatory Head of LIGO Livingston) and his wife Lisa (who is high up in LSU IT) are friends of ours I had already heard about it, but it is quite interesting that this is the type of "outside world" news that breaks through here.

vlicata Thu, 02/11/2016 - 16:30

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Antarctica: Cape Evans: Robert F. Scott's Base

vlicata — Sun, 07 Feb 2016 15:28:04 +0000

Antarctica: Cape Evans: Robert F. Scott's Base

Our most recent helo trip out from McMurdo on our NSF Artists & Writers Project took us to Cape Evans, the site of Robert Scott’s Terra Nova Hut, where they based their 1910-1913 trip to the South Pole. We went with Anthony Powell (the filmmaker from Scott Base who made the movie “Antarctica: A Year on Ice”. He has an engineering/tech “day job” at Scott Base and is a moviemaker in his off time). The Terra Nova Hut is the most elaborate and extensive of the 3 main historic huts in the McMurdo-ish area (the other 2 are Discovery Hut, right at McMurdo, and the Shackleton Nimrod Hut at Royds – described in earlier posts in this series). Here is a shot of the outside of the hut with Mount Erebus in the background.

The restoration work done by the Antarctic Heritage Trust is quite evident as the Hut is in absolutely great shape. Inside this hut there are many bunks, a full science lab (about the size of the average American home bathroom), a large dining table that easily seats 12, a variety of other work and storage areas partially or fully partitioned off. From just inside the the front door it is possible to go into the areas described above, or go around the outer section (still fully inside the hut but well separated from the rest by an inner set of walls) – this outer section contains the horse stables (where they kept 4-6 horses or “Siberian ponies”) and where the dogs were able to stay inside as well. Here is a photo of myself and Katy Jensen who is working with us inside the hut.

Here is a shot of one of the lab benches – they were doing so much science that this is actually an extra bench set up just outside the actual lab area in the hut. The lab area itself is roped off to block access, as are several other side rooms in the Hut (sort of like how the upstairs is roped off at Graceland).

Scott’s first expedition, the Discovery Expedition in 1901-1904, which established the Discovery Hut near present day McMurdo, apparently soon realized that the harbor area there froze over more often than expected (sometimes requiring ships to be “blasted” out of the ice, or be unable to get in close enough to dock) – so the Terra Nova Expedition established the hut at Cape Evans, about 12 miles away, where ship access was more consistent (although it is only 12-ish miles from McMurdo, after the sea ice starts to melt near the end of December it only gets accessed by helicopter as the overland route is much longer and quite hilly). The water was open on all 3 sides of Cape Evans while we were there (in early Feb).
Just over the hill we saw two Emperor penguins just hanging out behind a small ridge (keeping them out of the wind – the entire time we were there the wind was about 30mph with higher gusts – another day of never letting go of the tripod – and our big tripod weighs about 14 pounds and would easily be blown over in this wind). Mount Erebus is behind the penguins in this view.

It was nice to be able to go into the hut from time to time to get out of the wind for a few minutes. Even though the Terra Nova Hut seems like a small, self-contained city, and is surrounded by scattered historical artifacts all around it, again the sense of isolation is profound and present here, even for us. Even knowing that the helo was coming back a little after midnight (we had been dropped off at 7pm), even knowing that 3 of us had radios, or that if we needed, it was “only” an estimated 1-2 day climb (up and down hills) to get back to McMurdo, the wind and cold and scarcity of wildlife (2 penguins, about a dozen skuas, and 3 seals while we were there) – these things somehow conspire to give the feeling of only being connected to “safety” by a thin thread that might easily break at any moment. This feeling must have been amplified by so many orders of magnitude for the early explorers. I mean if this place, including McMurdo, routinely feels separated from the rest of the world on a moment to moment and day to day basis today, it is interesting to even try to imagine what it must have felt like for them. Even going to the moon, even eventual human trips to Mars, will not be as isolated from connection to the outside world as the early Antarctic explorers were. More soon...

vlicata Sun, 02/07/2016 - 10:28

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Antarctica: Dry Valleys

vlicata — Sat, 30 Jan 2016 15:00:14 +0000

Antarctica: Dry Valleys

On the next leg of our NSF Antarctic Artists & Writers project we flew to the Antarctic Dry Valleys from McMurdo. It is almost an hour helicopter ride across the ice shelf, and we hopped from site to site all day: landing at Lake Hoare for a moment to drop off someone and pick up Zach Sudman, a stream hydrologist who we spent most of the day with. We flew with Zach another 10 minutes to Lawson Stream – yes a flowing stream (from summer glacier melt) in the Taylor Valley. We video photographed Zach Sudman using surveying equipment to measure the height of the lake and the stream.

Here is a photo of Mike Johnson from the Stream Team research group at Lake Bonny camp checking a weather station.

The helicopter in the background took us back to Lake Hoare camp after spending about an hour at Lake Bonny so Mike and Zach could get their lake level measurements. Here is a picture of Mike and Zach at their Lawson Stream equipment box.

The box is located about 100-200 yards from where the helicopter lands and contains monitoring equipment that is connected to probes in the stream that measure stream temperature, flow, and depth. The box has been anchored in place there and working for about a decade as part of the gigantic LTER (Long Term Ecological Research) project in Antarctica, which involves many different researchers studying Antarctic ecology across the spectrum. Lawson Stream is not really visible in the above photo, but is about 3 yards to the other side of the box. The landscape shown is typical for the Dry Valleys – lots of “dry valley” punctuated by glaciers (small glaciers, but each has their own name – and a small glacier is still often bigger than an airport).

Here is a photo of me taking a photo near Bohner Stream.

This photo really shows the Martian like landscape of the Dry Valleys. While the Atacama desert in Chile has also long been used as an Earth-analog for Mars, now it's seem more the Antarctic Dry Valleys, as the cold makes it more analogous to Mars. If it looks isolated and lonely in this picture, it feels 10 times more isolated while there. Oddly, it doesn't feel lonely, but that seems to be because your mind makes an instantaneous strong connection to the people you are with on site. This is made easier by the fact that nearly everyone working at McMurdo is extraordinarily nice and interactive. At this site, the Stream Team finished their work early and called for a helicopter pickup. Trish had already headed up the hill to take some pictures when we got a call on the radio that the helicopter was landing immediately. Zach, Mike, me and Forrest (another Stream Team member) had to run full speed up a 100 yard sand hill to get to the helicopter. If you’ve ever run up a sand dune you know how fun that is – especially in big boots and with each of us carrying about 30 pounds of equipment. The helicopter pilots do not like waiting and want you to be in the landing area and waiting when they are still several minutes out. Helicopter landings in the Dry Valleys also consist of taking a sand and dirt shower. Zach and his colleagues showed us their technique for kneeling facing away from the helicopter as it lands (or as it leaves after making a drop off) with your jacket hood up as a good way to avoid a rock blasted face. More soon…

vlicata Sat, 01/30/2016 - 10:00

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Antarctica: Penguin Chronicles

vlicata — Tue, 26 Jan 2016 23:02:35 +0000

Antarctica: Penguin Chronicles

As part of our project we just flew to Cape Royds on a helicopter to take photographs of Dr. David Ainley among the penguins he’s studied for many years. It is about a 10 minute helicopter ride from McMurdo. We arrived in strong winds (maybe 30 mph? – enough to stop you from walking and have to brace yourself from being blown backward during gusts). The helicopter dropped us off and left, and after a short walk we arrived at Shackleton’s Hut (the nicest of the main huts on Ross Island). It’s beautiful and warm inside the hut. Despite the wind it feels comfortable and cozy inside, with lots of room and a high ceiling (with socks hanging on wires overhead – hundred year old socks – picture below).

About 100 yards beyond the hut is an Adelie penguin colony. David Ainley has been working with the penguins for decades and he was our host for this site. His group was collecting data on penguin chick development. The fuzzy gray chicks were almost the same size as the adults at this point, and David and his group spent about an hour capturing “random” chicks and weighing and measuring them. His unique method of picking a “random” chick goes like this: he mentally selects a chick somewhere on the cape, then asks someone nearby for a direction and a number, such as “right 3”. Then he collects the chick that is 3 chicks to the right of the one he had mentally selected. Nice method for keeping himself from introducing some sort of unconscious selection bias.

Here’s a nice shot of a group of penguins close up, and a group with a nice landscape behind. (Sorry if the resolution is not optimal, downloading and uploading from here is slow with large files so these are reduced).

While we were there, there was a lot of activity in the colony: arguments between chicks and adults (a particularly pushy chick chased an adult about 20 yards), two skua’s attacked and ate a chick, lots pebble collection trips occurred (the penguins roam around collecting small rocks (about half the diameter of a pingpong ball) and gathering them into a circular nest one layer of rocks thick. The feeling of isolation was extraordinary. The temperature was quite nice, but the wind made making our slow motion videos difficult. We videotaped Dr. Ainley among the penguins in several different poses similar to photographs of Herbert Ponting among the penguins from this very same colony 100 years ago. We even identified particular boulders in Ponting’s turn of the century photos and Dr. Ainley posed with the penguins near the same boulders. It’s quite bizarre to realize that this same site has hosted this Adelie colony for over a hundred years, and that we were walking over a landscape that had barely changed in that time. The penguins are not afraid of us. They barely care while Ainley walks among them – they get a little perturbed and move out of the way, but that’s about it. They seem like a happy but fragile lot. To watch them, it feels like if they weren’t here in this barely accessible place, that they would have been wiped out decades ago by human intervention. They are curious and like to wander up behind you or beside you while you are working, but when you then turn and look at them they sort of shrug and move along. There is a small lake between the colony and the Shackleton Hut named “Pony Lake”. Ainley says this lake is so filled with penguin guano that it has a high urea content and can be used as a solvent that will clean just about anything. (Maybe it would also denature proteins). Without a special permit, however, you cannot take a sample from the lake (we had to have a permit just to go to this site and walk around).

This was the first of the “out of town” filming sites for our project.

And here’s two goofy people (Trish and I) blocking the nice landscape to pose with the penguins. The penguins don't seem to mind.

More soon…

vlicata Tue, 01/26/2016 - 18:02

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Antarctica: Arrival

vlicata — Fri, 22 Jan 2016 13:29:51 +0000

Antarctica: Arrival

Hello again,
We’ve been on Mars – er, I mean in Antarctica for 1 week now. It’s similar to what one might imagine being on Mars is like, but with breathable air (nice air). The landscape around McMurdo Station is all volcanic rock. Rock and dirt everywhere. Stand in the middle of McMurdo and spin around and you’ll see about 230 degrees of rock and dirt as far as the eye can see, and about 130 degrees of extraordinary beauty looking across the Ross Ice Shelf toward the Trans-Antarctic Mountains. Right across from the station, shown in the picture, is Mount Discovery (slightly obscured in clouds, the things that look like slugs on the ice are seals). In the other direction you mostly see dirt.

The name of the game upon arrival in McMurdo is: training! Upon arrival (after an 8 hour flight in a C-130 Hercules) we went immediately into a welcoming briefing followed by a day that included a science briefing, an environmental briefing (to review the quite strict environmental restrictions here – e.g. no peeing outdoors anywhere), a tour of Crary lab (where all of the lab work at McMurdo takes place and where our office is) along with a lab policies briefing, a 3.5 hour field safety course (that included learning how to use a survival bag, set up a survival tent, and light the mini-stove in the survival bag). (The word “bag” makes it sound small and light – it is actually about a 50 bag full of stuff that is required to be taken along on any trips outside of McMurdo. Each “survival bag” supports 2 people for about 5-6 days).

The next day we got “core” training – including both standard operational procedures for a variety of “daily” tasks in McMurdo (such as throwing away anything), and training on how to use and do a safety check on trucks and vehicles (they use a unique, specially installed parking brake system here called a MIDI brake – which is not supposed to freeze whereas a normal parking brake would). We also got an “outdoor recreation” briefing, to tell you what you can and cannot do in the area (not a lot: you can walk on almost any road (all dirt roads, a small network in town and one road going to Scott Base and to Willy Field (the airport)) or you can walk on about 4 trails in the area. There are a number of “indoor recreation” centers, however, including a couple of gyms, a weight room, a movie theatre, and so on (the famous McMurdo bowling alley is now gone).

One of the hikes you can do is out to Hut Point, where the Discovery Hut is. This hut was constructed on Scott’s Discovery Expedition in 1902, and was later used by Shackleton as well. The photo shows a view from Hut Point with the Discovery Hut in the foreground and McMurdo Station behind it (this view shows some of the more "Mars-y" landscape around McMurdo Station).

We (Trish Suchy and I) have also been trained to be “Hut Guides” – meaning we are now able to get the key to and give mini-tours inside the Discovery Hut. Some of the people who hike over to visit the hut know absolutely nothing about it, and others are encyclopedic in their knowledge of it. Our job as “hut guides” is primary actually “hut security” – reminding people not to touch anything in the hut (it is left exactly as it was in 1917 when it was used for the last time – there’s even food in the pot on the stove --so you know it was men who lived and worked here – I mean: who comes to Antarctica to do dishes?). We have to report any touching incident in the hut, accidental or otherwise. The hut is filled with frozen but slowly rotting seal meat, which has a uniquely unpleasant odor (although some people say they like it). Yesterday, while marginally assisting two much more experienced hut guides, we all got to see a small group of Adelie penguins (six of them) having a stroll over the ice near the point. None of us had anything other than a cell phone camera with us at the time. But we’re scheduled to get some real penguin shots at Cape Royds soon. Until next time…

vlicata Fri, 01/22/2016 - 08:29

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Dance Your Ph.D. - 2013 Winners Announced!

vlicata — Thu, 21 Nov 2013 15:30:38 +0000

Dance Your Ph.D. - 2013 Winners Announced!

It's time again for John Bohannon's annual "Dance Your Ph.D." contest. This year, in my opinion, there are even more high quality entries than in previous years! (I was one of the judges who did the first round of choices...the "winners" were then chosen by a panel that includes several professional dancers (for several years it has been members of Pilobulus)). And they are all now posted online ("winners" at the link above - all the videos are posted here - because really they are ALL winners in my opinion.

And if you can come up with more difficult ways to try to explain science - we could start some other awesome contests. Explain your Ph.D. in poetry. Design a dress or suit that explains your Ph.D. Knit your Ph.D. Origami your Ph.D. Puppet Theatre Your Ph.D. Stop-Motion Animate Your Ph.D. Ballon Animalize Your Ph.D. But until then...

Dance! Dance! Dance!

vlicata Thu, 11/21/2013 - 10:30

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Paper Up: Correlations between DNA binding thermodynamics and DNA polymerase activity

vlicata — Sat, 14 Sep 2013 17:28:48 +0000

Paper Up: Correlations between DNA binding thermodynamics and DNA polymerase activity

Our lab has a paper called: "Enthalpic Switch-Points and Temperature Dependencies of DNA binding and Nucleotide Incorporation by Pol I DNA Polymerases" that was just published in BBA (Biochimica et Biophysica Acta): Proteins and Proteomics. The study follows up on an observation and prediction we had made some years ago in a different paper.

The study deals with quite a lot of rather detailed thermodynamics of DNA binding (free energy, enthalpy, entropy, heat capacity…) and looks for correlations between such thermodynamic measurements of binding and the functional behavior of a couple of similar DNA polymerases. DNA polymerases are the enzymes that replicate DNA. The strong correlation that we found was between entropy (ΔH) of binding and onset of functional replication activity. Or to state it another way:

As the temperature increases, the enthalpy of binding of the polymerases to DNA goes from positive (unfavorable = heat input required) to negative (favorable = heat released). Right at the temperature where the binding enthalpy switches from positive to negative, the replication activity of the polymerase effectively switches "on". So, the polymerases bind to DNA quite fine at lower temperatures, but are effectively "shut off" functionally until after the temperature where the ΔH of binding switches from positive to negative. And this temperature is not the same for each polymerase – it is specific to the particular polymerase. This correlation is illustrated in the figure below:

So what does this mean? We believe it means that the simple binding of an enzyme to DNA is not sufficient for that enzyme to carry out its catalytic function on the DNA, and that the balance of different types of binding energy (enthalpy versus entropy) may dictate when a bound enzyme is turned "off" versus turned "on". While this is the only set of DNA binding proteins where applicable overlapping binding and activity data have been compared, we hypothesize that this correlation may hold for many DNA-binding enzymes.

It is also interesting because a few other studies in some very different systems have also recently been finding that for some processes, following the enthalpy is much more important than following the free energy (ΔG) (the free energy is what biochemists "follow" for mechanistic clues 99% of the time). We mention other examples in the paper, but a particularly interesting one is the finding that the efficacy of HIV protease inhibitors also tracks with enthalpy of binding, and not with the free energy of binding (Freire, Drug Discovery Today 13:19 (2008)).

So why does switching from positive to negative enthalpy effectively switch "on" the protein activity? Good question, we'd love to know the answer. We postulate a few possibilities in the paper – one of which being that maybe the catalytic reactions just need a little heat, and a negative binding enthalpy will release a little heat.

The data in our paper also speak to a longstanding concept in extremophile research: something called the concept of "corresponding states". This concept states that a protein from a thermophile (a high temperature organism) will function "normally" only at high temperatures. According to the corresponding states theory, our thermophilic polymerase should not bind DNA at all at lower temperatures, and should not show "normal" nucleotide activity until quite high temperatures. Our data show that neither of these "corresponding states" predictions is true, and suggest that the situation is somewhat more complicated than "heat up the protein and then it will behave like the lower temperature version of the protein". The corresponding states theory has been challenged by a few different studies over the past decade, but it turns out that for a variety of reasons it is actually difficult to get appropriate data to properly refine it. It is one of those theories that must wait a little longer for experimental technology to catch up to it for it to be appropriately tested and refined.

As always, if would like a copy of the paper and you cannot get it free from the link above or your library, I will send you one.

vlicata Sat, 09/14/2013 - 13:28

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Dear Prof. LiCata,
Thanks a lot for this popular explanation of your article. It became a bit clearer now.
However, when I read your article I was looking for the answer whether overall stability of primer-template duplex may determine the likelihood that the polymerase binds to a duplex.
Do I understand correctly, that you studied only perfectly matched DNA duplex?