Teaching and tweeting

MOR tweet

It’s been a while since I’ve been a TA in the traditional sense – you know, sitting in class, running and grading labs, answering questions from inquisitive minds (or at least referring them to smarter people than myself)… So I’m pretty excited to be back at it this quarter. Yesterday was our very first class and today is our first lab – huzzah!

I decided yesterday, somewhat on a whim, to take the class to Twitter – I’ll be tweeting class-related goodies using the hashtag #Ocean410TA, in case you want to follow along – whether you’re in the class or not. I’d be stoked to hear from people who are just curious about what we’re doing. The class is a senior level (4th year for you Canadian friends) marine geology and geophysics class – we basically learn about how the ocean basins form, and why the look like they do. Underwater earthquakes and volcanoes! The coolest.

Has anyone out there tweeted a class before? Any advice or thoughts?

And in case you’re wondering why scientists should tweet, check out this blog post on the AGU website and another one on the Deep Sea News site.

Learning to write

PickAPen

I took a writing class!  Yes I did.  I probably shouldn’t admit it, really, because now you’ll all expect me to have improved immensely, and that makes me nervous.

The class was with Stacey Solie (@StaceySolie), and it was fantastic. I learned a lot and here are a few of my favorite tips:

Freewriting: Every day, set aside a dedicated chunk of time to just write.  Don’t worry about punctuation, spelling, grammar, or anything.  It’s great for writer’s block: you don’t even need to start at the beginning or anything.  It just helps get the ball rolling and get you out of whatever funk you’re in.  I’m trying to do at least 15 minutes per day (minimum).

Read your work out loud:  Admittedly, this is one that I knew about before, but it bears repeating.  I don’t do it nearly enough and I really should because when I do, I always catch mistakes.

Stop apologizing for your work: It’s a terrible habit of mine and doesn’t really accomplish anything.  For example, when giving an essay to someone to proof-read, it’s pointless to say things like, “Oh, here you go. It’s really bad, sorry.”  It’s probably got some bad parts, and some good parts, and whoever is reading it will figure it out without you telling them.

So I’m working on building confidence in my writing…

Confidence

 

Know when to stop:  Try to recognize when you reach the point when your ongoing efforts cease to result in significant improvements. The “sweet spot”.  Stacey talked about this, and so did one of our guest speakers, Katie Arkema.  Here’s my own interpretation, in graphical form:

ListenToYourBladder2

Bonus materials!

Thanks to the terrific @realscientists followers, who pointed out a couple of important points that I missed before!

READ! Yup, to become a better writer, you have to read. A lot. I mean, you should read every day, and be critical about it, too.  Ask yourself, what is it that makes a certain piece of writing excellent or terrible? What techniques does the author use? Is there anything about their writing that could be improved upon? These observations will all eventually sink into your brain and make their way into your own writing. Hopefully not word for word though, because that’s not cool.

Practice. This sort of goes with the “free-writing” point above, but let’s give it a whole section unto itself. Because that’s how important it is. Like many skills, it’s more about hard work than innate genius. Have you read that book, Outliers, by Malcolm Gladwell? In it, he talks about what all of these wildly successful people have in common. Sure, there are loads of factors that lead to success, but the one in common between them all was that they’d put a metric butt-load of hours into their craft. Ten thousand hours, minimum, to be exact. So put in your time!

Well there you go.  You know I’m not a writing expert, I’ve just listed/regurgitated things that I thought were useful or inspiring. Hope it helped! Feel free to add to the list in the comments. 🙂

 

 

Whales in a Noisy Ocean

Noisy-Neighbors_600px

In the ocean, sound rules.  Unlike on land, where animals (just like us humans!) get a lot of information from light, animals in the ocean have evolved to take advantage of sound, which is much more effective than light under water.  Light gets absorbed quickly, but some sounds, like the low-frequency calls of blue whales, can travel hundreds of kilometers under water, under the right conditions.

Whales have developed really fascinating ways of using moans and clicks and songs to help them get the things they need in life – friends, mates, food… what more could a whale want?  Some whales find food by making sounds and then listening for echoes that bounce off of their prey.  Using those echoes, they can figure out where their food is (mmm, delicious fish!).  Whales can also use sound to communicate with each other.  A mother and calf might need to keep track of each other as they swim.  Or a male might show off his sweet singing voice to attract a female.

comms3panel

Unfortunately, noise in the ocean is on the rise, and it’s making life tougher for whales. Some of the sources of human-caused noise include ship traffic, seismic exploration for oil & gas and sonar testing. It’s worth noting, though, that there is noise in the ocean that is not caused by humans. Earthquakes, volcanoes, breaking waves, rain and even lightning are some of the things that add to the background noise. The thing is, whales have spent thousands of years evolving to deal with these natural noise sources – but in the last few decades they have suddenly had to get used to the growing din caused by human activities. And, as Chris Clark from the Bioacoustics Research Program at Cornell University explains, “it’s not just one ship. It’s ten thousand ships”. It’s the same as if only one person litters on the side of the road, it might not be such a big deal. The problem arises when everyone does it, all at the same time.

Noisesources

Scientists are still not sure exactly how noise affects whales – different whales might be more or less sensitive to particular sounds, and might respond in different ways. For example, right whales in the Bay of Fundy showed lower levels of stress hormones when ship traffic stopped briefly following the 9-11 terrorist attacks [1]. Killer whales off the coast of Washington state and British Columbia have increased the volume of their calls so that they can be heard above vessel traffic [2]. And in the most severe cases, some beaked whale strandings have been linked to mid-frequency naval sonar operations [3].

Excessive noise in the ocean causes a sort of masking effect – meaning that the noise is loud enough that the whales can’t hear what they normally would need to hear in their environment, whether it’s echoes from fish, or a signal from another whale. Not being able to find a mate or find food or find each other is a serious problem, especially for species that are already endangered.

But there is still hope. Now that we’re starting to realize how harmful noise can be, we’re finally in a position to actually do something about it. Small steps can make a big difference. Even slowing ships down can substantially reduce the overall noise. In recent years, the US Navy has funded a lot of basic research that has taught us a huge amount about how marine mammals hear and use and produce sounds. We’ve still got a long way to go, but now that we’re aware that there is a problem, we can work on ways to fix it.

This post was done with help from Chris Clark and Kevin White from the Bioacoustics Research Program at Cornell University.  The PDF version can be downloaded here.

References

[1] http://news.sciencemag.org/sciencenow/2012/02/shhh-ocean-noises-stress-out-wha.html
[2] Holt, Marla M., et al. “Speaking up: Killer whales (Orcinus orca) increase their call amplitude in response to vessel noise.” The Journal of the Acoustical Society of America 125.1 (2008): EL27-EL32.
[3] D’Amico, Angela, et al. Beaked whale strandings and naval exercises. Space and Naval Warfare Systems Center, San Diego CA, 2009.

What does a fin whale call sound like?

If you play back this audio file, you’ll be listening to a couple of fin whales and an earthquake, and according to my dog, that’s some exciting stuff. No, seriously, I played it on my laptop the other day, and Trooper got all agitated, and started growling and barking in what I can only assume was confusion. (“where’s the fin whale?? it’s got to be around here somewhere!”)

The colorful figure at the top of the post is called a spectrogram.  Time marches across to the right.  Frequency increases upward.  And the colors basically indicate loudness – brighter colors are louder.  This particular chunk of data was recorded in the dead of winter just off the coast of British Columbia, Canada, under more than a kilometer of water. Even though the instrument is designed to measure earthquakes, it also picks up the very low, booming calls of fin and blue whales.  The spectrogram shows two slightly different calls alternating – one slightly higher pitched and one slightly lower.  We believe this is probably two fin whales passing near the seismometer.

You might notice that the audio clip is about 30 seconds long, but the spectrogram shows five minutes of data – that’s because the calls are down around 20 Hz, which is at the very lower end of the human hearing range.  (If you have tip top hearing, you are probably sensitive to sounds between 20 Hz and 20 kHz.)  I sped up the audio by a factor of 10, so that we can actually hear it – bloop… bloop… bloop…

At about 10:03am in the spectrogram, and 20 seconds into the audio recording, you can see/hear an earthquake in the background.  My seismologist colleagues tell me that this isn’t the distinctive crack of a primary or secondary phase arrival from an earthquake, but possibly the rumbling caused by a tertiary, or “T phase”, arrival.

So why did Trooper have a meltdown?  I guess you would too, if you thought you were suddenly surrounded by a couple of super high-pitched fin whales and an earthquake.

The mystery of the shifting tropical rain belt

from nsf.gov (credit: Pacific Worlds)
From nsf.gov

This week’s science+comics interview is brought to you by Yen-Ting Hwang, a UW Atmospheric Sciences student in the final year of her PhD. Ting’s work is focused on large-scale climate dynamics.

The Sahel region in Africa is a semi-arid boundary along the southern edge of the Sahara desert. The people living in this region are balanced on the very edge of habitable terrain, and rely on a short annual rainy season for their crops to grow. The slightest shift in annual climate can result in devastating crop failures and ultimately widespread famine. During the second half of the twentieth century, the region was hit by year after year of drought.

For her final thesis chapter, Ting has tried to understand why that drought might have happened when it did. The life-sustaining annual rainfall in the region occurs as part of a seasonally migrating tropical rainfall pattern. Scientists call this the ITCZ, or the inter-tropical convergence zone, and it’s a rain band that circles the globe like a belt. Solar radiation near the equator is far stronger than at the poles, and when the moist air near the equator is heated, it rises. The rising air eventually reaches an altitude where it’s cooled, and the moisture that was carried aloft condenses to form clouds and rain.

This air is transported poleward at high altitude until it reaches about 30 degrees latitude either north or south, at which point it sinks down toward the earth’s surface. The air then moves back toward the equator, picking up moisture along the way. This cycle is called Hadley Cell circulation.

Hadley-Cells_600px

By piecing together climate observations, scientists know that the drought in the Sahel region between about 1950-1990 was related to a very slight southward shift of the tropical rain belt. This type of shift happens when the temperature difference between the northern and southern hemispheres changes. If the northern hemisphere is cooler, the northern Hadley cell will strengthen as it tries to pull warm air up from the south, and the tropical rainfall band will shift southward.

To answer this question, Ting compared results from twenty different IPCC models (IPCC = Intergovernmental Panel on Climate Change). She looked at a variety of different possible factors that could result in an uneven heating or cooling of the planet between the northern and southern hemispheres – things like clouds and ocean circulation. The factor that showed the strongest correlation was surprising: it was the aerosols!

Aerosols are basically tiny particles that are suspended in the air. Naturally occurring aerosols are always floating around our atmosphere – dust from deserts, smoke from forest fires, and even sea salt. But there are also anthropogenic aerosols – the ones that occur as a result of pollution. There are different types, but Ting found that the strong correlation was with sulfate aerosols, which are white in color. These aerosols have two main effects:

a) They reflect sunlight, which means less sunlight reaches the earth’s surface.
b) Aerosols in the air tend to cause clouds to persist for longer than they would other wise – you might imagine droplets of water staying aloft when they have a handy bit of sulfate to stick to.

Overall, both of these lead to a cooling effect.

Aerosols don’t stick around in the air for long though, and they don’t travel far from their source. It’s a bit counterintuitive to imagine that the smog from an American or European factory could be affecting tropical precipitation. But the slightest shift in the temperature balance between the northern and southern hemispheres is all it takes. Here’s a cartoon showing the basics of how this works:

Aerosols_600px

While the Sahel region was being decimated by drought in the twentieth century, industrialization in developed countries was on the rise.   Since most of the industrialization happening at the time was in the northern hemisphere, that hemisphere was cooler than it otherwise would have been.  And model results indicate that this change was enough to shift the tropical rain band southward.  By the 1980s and 1990s, air pollution was widely recognized as being harmful, and various environmental regulations were put into place.  And, lo and behold: that’s about the same time that the ITCZ shifted back to its previous position.

More recently, Ting has been looking at how we can use climate models to predict how the tropical rainfall band might shift or change given different climate scenarios that are tested by IPCC models.  Of course, the effect of aerosols is only one piece of the puzzle.  The northern hemisphere cooling that Ting was investigating was overlaid on an overall warming trend.  The northern hemisphere was actually warming between 1950-1990, just not as quickly as the southern hemisphere.  In fact, recent studies indicate that the northern hemisphere appears to be warming more quickly, which may have significant consequences for tropical precipitation patterns.

To learn more about Ting and her lab group, check out these links:

http://www.atmos.washington.edu/~yting/

http://www.atmos.washington.edu/~dargan/

Press releases about some of their other work:

http://www.washington.edu/news/2013/03/11/remote-clouds-responsible-for-climate-models-glitch-in-tropical-rainfall/

http://www.theverge.com/2013/3/25/4129026/clouds-are-hiding-the-the-truth-of-how-much-earths-climate-will-change

http://newscenter.berkeley.edu/2013/04/02/shifting-rainfall-patterns-in-tropics/

Also, this paper is in press, so you can read all the details soon!

Hwang, Y.-T., Frierson, D. M. W., and S. M. Kang. Anthropogenic sulfate aerosol and the southward shift of tropical precipitation in the late 20th century. in press, Geophysical Research Letters

Stars in the Andromeda Galaxy find the fountain of youth

starcomic

This science+comics post takes us where this blog has never gone before:  to outer space.

Phil Rosenfield is a PhD candidate at UW in the department of Astronomy, and studies stellar and extra-galactic astrophysics (woah).  He uses data collected on the Hubble Space Telescope to look at stars in distant galaxies and is particularly interested in how stars change over time.

One of Phil’s interests is in the Andromeda Galaxy.  Here’s a photo – breathtaking, isn’t it?

Andromeda_Galaxy_600px
image from https://en.wikipedia.org/wiki/File:Andromeda_Galaxy_%28with_h-alpha%29.jpg, shared under Creative Commons license by Adam Evans

The Andromeda Galaxy, like other galaxies, is a cluster of stars and dust and gas and dark matter.  And get this – it’s the farthest thing you can see with just your eyes from Earth.  Wow, now that’s crazy!  If you go out on a clear night in late summer or early fall, you can find it for yourself, using these steps from Phil’s blog.  And while you’re gazing at that tiny speck in the night sky, know that the light hitting your eyeballs from this particular galaxy actually left it 2.5 million years ago – back when our earliest ancestors were just figuring out how to use primitive tools to help them scavenge for food.

Phil and his lab group are working with data collected on the Hubble Space Telescope (a.k.a the HST, if you’re hip with the Hubble lingo).  The HST orbits around the earth about every 97 minutes.  As a scientist, if you want to get the HST folks to take a particular set of images, you need to put together a proposal – usually with a large group of scientists who are interested in the same thing.  Julianne Dalcanton, the head of Phil’s lab group, and several other scientists, successfully convinced the folks at Hubble to capture super-detailed images of the Andromeda Galaxy.  These images are being collected over a total of 828 HST orbits over the course of four years.

The Andromeda Galaxy is shaped sort of like a spiral-y pancake, a flattened disk with a bright bulge in the middle.  New stars tend to form in the disk part of a galaxy, and closer to the bulge you’d normally expect to see older stars. So how do you know whether a star is young or old, just by looking at it?  The main way to tell the difference is by looking at the frequency of light that is emitted.  Young, massive stars are mostly emitting light in the ultra-violet (UV) part of the light spectrum – if you picture the violet part of a rainbow, ultra-violet would be the next color past violet, which our eyes can’t even pick up. Older, not as massive stars, on the other hand, emit most of their light in redder parts of the spectrum, like our sun, which emits most of its like in optical frequencies.

The first zoomed-in image that the HST collected of the Andromeda Galaxy was near the central bulge.  As an astronomer, you would not expect to find stars emitting UV light from so near the bulge.  But when Phil’s group started doing analysis on the image, they were surprised to find that there were LOTS of stars near the bulge with the characteristics of young stars.  But they couldn’t be so young so near the bulge – star formation doesn’t happen there.

To explain this discrepancy, astronomers have figured out that there must be a completely different type of star.   Here’s a figure describing the “normal” life history of a star, and then the life history for the “new” type of star.  Here’s a figure comparing the two paths that a star might take, if it started out about the same mass as our sun.

LifeOfAStar

Learning about what is happening in a nearby galaxy like Andromeda can help astronomers understand where the light is coming from in more distant galaxies where even the HST can’t make out individual stars. If Phil’s group can confidently say how old stars like these are, then they can use that knowledge to help them interpret light from other galaxies that have this strange amount of UV light in their centers. They can then begin to address some big questions, like: how and when did galaxies form? And how old is our universe? The results of this analysis give astronomers a way to independently test other methods that are used to answer these kinds of questions.

If you want to know more about Phil’s work, check out his blog: https://sites.google.com/a/uw.edu/philrose/blog, especially his post on Bright UV stars in the bulge of M31 (Andromeda Galaxy).

Seismic tomography: the easy way

When I was an undergrad, I had to take a year of geophysics, and on the first day, the professor explained that geophysics meant finding things underground without digging.  The rest of my lab group here at the UW are all marine geophysicists, and they routinely have to find things underground without digging, but with the added complication of having to get through a couple of kilometers of water, too.

You may remember my interview with Rob Weekly a few weeks back. This week’s interview is with my office-mate, Dax Soule. Dax studies marine geology and geophysics in the School of Oceanography at the University of Washington. Like Rob, he focuses on active source seismology. In fact, he’s looking at some of the same data as Rob, just different parts. And since we already went over a lot of the basic background in Rob’s post, I’m going to jump right into some fun tomography stuff. In a nutshell, tomography means building up a 3D picture of what’s underground by measuring how long it takes for seismic waves to travel through. In tomography, you’re not sampling the material directly, but you’re measuring how the seismic velocity varies. Seismic velocity is a measure of how quickly a seismic wave can travel through a certain type of rock, so if you know the velocity structure you can make inferences about the geological structure.

Imaging the earth’s crust

When you’re doing seismic tomography, it’s a bit like peeling back the layers of an onion: you have to figure out the shallow stuff before the deep. Rob’s work focused on obtaining a three-dimensional seismic velocity structure from the seafloor down to about 2.5-3 km depth. Dax is taking Rob’s results and extending downward to include the entire depth of the crust. He’s looking between the seafloor and the Mohorovicic discontinuity, or the “Moho”, which is the boundary between the earth’s crust and the mantle.

In seafloor maps of the region, you can see that there’s a bathymetric high – a plateau where the water depth is shallower than the surrounding seafloor. A seismic reflection study a few years back [1] showed that this plateau likely corresponds to a thickening of the oceanic crust at this location. Dax’s tomography work will help to clarify exactly what’s going on, and will give a more detailed picture of how the crustal thickness varies in the area.

Dax explained that measuring crustal thickness variations near a mid-ocean spreading center can tell you about how that crust was produced – was a episodic or constant? And where was the source of new crust – was it on the axis of the ridge, or off-axis?

How the experiment works

Here’s a little cartoon showing the basic geometry of the seismic experiment.SeismicRays_600px

A seismic source is generated near the sea surface, and the energy travels through the water column and into the sea floor. Once in the earth’s crust, the energy is converted into to types of waves: primary waves (p-waves) and secondary waves (s-waves). There are many different types of paths that these waves can take as they travel through the earth, and each type of path is known as a “phase”. In the above figure, the two phases that are shown are Pg and PmP. Rob used the Pg phase arrivals to image the upper portion of the crust. Dax looks at the PmP phases, which are the ones that bounce off the Moho.

Dax goes through the data and manually picks out the PmP phase arrival times. This part of the job is not the most exciting, but someone’s got to do it! Fortunately, all that work does pay off, and once Dax has his picks, he can start digging into the tomography part of his work.

Five easy steps
Here’s a handy-dandy summary of the steps that Dax goes through to build up a tomographic inversion.

five-easy-steps_600px

So that’s what my office-mate does… good to know!  Dax is still working through the data and the very complex inversion code, so stay tuned for a future post on what he finds deep in the crust, and what the crustal thickness can tell us about seafloor production at the Endeavour Ridge.

Reference
[1] Carbotte, Suzanne M., Mladen R. Nedimović, Juan Pablo Canales, Graham M. Kent, Alistair J. Harding, and Milena Marjanović. “Variable crustal structure along the Juan de Fuca Ridge: Influence of on‐axis hot spots and absolute plate motions.” Geochemistry, Geophysics, Geosystems 9, no. 8 (2008).

When the wall comes tumbling down: Elwha River sediment transport

Elwha River Valley from Hurricane Ridge (Photo by Steve Voght, http://www.flickr.com/photos/voght/2720398016/in/set-72157606472551601)
Elwha River Valley from Hurricane Ridge (Photo by Steve Voght, http://www.flickr.com/photos/voght/2720398016/in/set-72157606472551601)

If you live in western Washington, you are probably aware that the biggest dam removal ever done in the US is happening right in our back yard.  Nearly one hundred years ago, developers on the Olympic Peninsula wanted to harness the hydroelectric power of the Elwha River.  They built two dams: the Elwha Dam, eight kilometers upstream from the ocean, and the Glines Canyon Dam an additional thirteen kilometers further up.  Unfortunately, the builders ignored permitting requirements, and did not make any accommodation for fish passage. The dams failed a safety review in the 1970s and in 1992 Congress passed the Elwha River Fisheries and Restoration Act.  This eventually led to the decision to remove the dams entirely rather than to attempt the difficult and expensive task of bringing them up to code.

ElwhaDamFish

Together, the two dams blocked a full 90% of the watershed’s fish habitat, and were holding back enough sediment to fill more than 10,000 Olympic-size swimming pools.  Planning their removal was not a trivial task.  It’s sort of a goldilocks scenario:  take them out too quickly and there’s a danger of flooding.  But take them out slowly, and it can be bad for fish because of prolonged turbid conditions.  After much careful deliberation, a 2-year period of dam removal was deemed just right.

Elwha_map_600px

Emily Eidam is a 2nd year graduate student at the University of Washington, in the Marine Geology and Geophysics option within the School of Oceanography.  She is looking specifically at what is going to happen to the mud that leaves the reservoirs during and shortly after dam removal.  How will that sediment be transported and deposited in coastal waters?  At this point, the lower dam has been completely removed, and all that’s left of the upper dam is a short chunk due to be removed with explosives this summer.  But what a last portion it is:  piled behind what remains of the Glines Canyon Dam is the mother lode of sediment.  Once it goes, Emily and her colleagues expect a large flux of muddy sediment to flow seaward.

Emily, a geologist and civil engineer, says that this is what she’s waiting for: the big pulse of muddy sediment.  When river water flows into the ocean, it is usually less dense than the salty seawater, forming a plume over the surface.  But sometimes, as a result of a big storm or a landslide, the river water takes on an unusually high volume of sediment and briefly becomes denser than seawater, plunging down instead of floating at the surface.  Geologists know that this happens, but don’t fully understand how it works because it’s incredibly difficult to capture these super dense, or hyperpycnal flows.  They don’t happen often, and when they do they only last for a few hours to a few days.

elwha-plume
Sediment plume flowing out from the Elwha River into the Strait of Juan de Fuca (http://gallery.usgs.gov/photos/10_22_2012_kof6IVt22C_10_22_2012_0). This is a surface plume, and although this aerial photograph looks dramatic, it’s difficult to tell where all that sediment will be deposited without taking in situ measurements.

In a way, the Elwha River dam removal provides the perfect opportunity to study hyperpycnal flows, because it’s creating ideal and predictable conditions for such flows to happen.  To ensure that they capture an event, Emily and her lab group have rigged up special tripods that sit on the seafloor and measure, well, just about everything a marine geologist could possibly want.  Video cameras record suspended sediment particles.  A variety of oceanographic sensors measure everything from temperature and salinity to current speed throughout the water column.  The “murkiness” of the water is estimated using instruments that send out a burst of light, and measure how much is scattered back by suspended particulate matter.  Sediment collected in traps provides data on size distributions of settling material.

hyperpycnal

In addition to the data collected on the tripods, Emily and her lab group conduct ship-based surveys several times per year, taking additional oceanographic measurements, and also collecting sediment samples from the seabed.

Because of the difficulty in predicting when and where they’re going to happen, real-time measurements of hyperpycnal flows are sparse (at best) – so capturing one will be amazing!  But in the meantime, they are collecting an enormous dataset that can be used to understand where sediment leaving the river gets deposited, and how it gets there.  Most of us don’t spend much time thinking about how sediment from a river becomes part of the seabed, but understanding how it works can help scientists interpret geological records that contain clues about ancient coastlines and rivers, changes in sea level, and even past climate.

Want to keep up with Emily and her lab group’s adventures?  Check out their website and blog.  The Elwha project was also recently featured on UW News.

Learn more about Elwha River history and dam removal:
http://www.elwhabiodiversity.org/elwha/
http://www.video-monitoring.com/construction/olympic/js.htm
http://www.coastalwatershedinstitute.org/projects.htm
http://www.pbs.org/americanfieldguide/teachers/salmon/history.pdf

claimtoken-515c64eba5e9b

Diatom survival: It’s in their genes

Please welcome Sara Bender to the Science+comics interview series!  This week we’re taking a peek into the world of diatoms, and how they take up nutrients. Check it out!


Diatoms are tiny, single celled organisms that live near the surface of the ocean.  They are a type of phytoplankton, which are small, drifting organisms that form the base of the marine food web.  Many of them are so tiny that they can’t even be seen with the naked eye – even smaller than the width of a human hair.  Although they are not plants, they use photosynthesis to drive their metabolic processes, taking in carbon dioxide and releasing oxygen.  Also, like plants, they need nutrients such as nitrogen and phosphorous to survive.  Because of coastal upwelling and runoff from land, shallow, coastal regions tend to have the highest nutrient concentrations, and also the highest diatom concentrations.

Sara Bender studies phytoplankton ecology with the Armbrust Lab, and is a PhD student in her final year of Biological Oceanography at the University of Washington.  One of the things that Sara has looked at is how diatoms take up nitrogen. How do they do it, and how have they adapted to the conditions that exist at different locations? Sara has looked at three species in particular, all from very different environments. In a way, these species are sort of like the “lab rats” of the diatom research world, and many researchers have used them for experiments in the past and present. Let’s meet Sara’s special “pet diatoms”, shall we?

Diatom-characters

Now, here’s where Sara’s research gets really interesting: she uses cutting edge techniques developed for the medical field, and applies them to her pet diatoms. Her advisor, Ginger, along with a team of researchers, actually sequenced the very first diatom genome (Thaps) in 2004! Since then, both Fracy and Psemu have also had their genomes sequenced, and the number of diatom genomes is on the rise!

So how does Sara use these genetic sequences to learn about diatoms? Well, let’s back up a bit and talk about what is in a genome. DNA is made up of a specific sequence of nucleotides. You can think of these nucleotides as a very short alphabet – one with only four letters: A, T, C, and G. These letters are grouped together into genes that form the genome, which contains information that the cell can use to carry out different operations. Sara is interested in a particular type of operation: she wants to know how diatoms pull nitrogen out of the water. She asks questions like: how have different diatoms adapted to different conditions? And how might diatoms respond if conditions change in the future, as a result of climate change, for example?

diatom-genes

Sara looks for similarities and differences between genes from her three test species. And as it turns out, just because different organisms have some of the same genes, it doesn’t mean that they express them in the same way – or at all. After looking at which genes are present, Sara is able to form hypotheses. For example, let’s say that one diatom has ten of a specific type of nitrogen transporters, and the other two diatoms only have one of those, you might guess that the diatom with the ten transporters had to adapt to some particular condition in its environment.

Diatoms-chat

To test her hypotheses she looks at the next step in the process: the gene transcription step. This is where the information contained in genes gets transcribed into RNA. If this happens, the RNA can be translated into a protein, which can then be used to carry out some cell function. Sara looks at whether particular genes get transcribed in order to better understand how the cell functions under certain conditions. She can simulate different environments in the lab and then look at how the diatoms react based on the level of gene transcription.

Since diatoms play such a significant role in the marine food web, it’s really important to understand how they might be affected by changes in the ocean – whatever happens to them can have cascading effects on other organisms higher up in the food web.

Sara will be graduating this summer, and after that she’s going to the Woods Hole Oceanographic Institution (WHOI) to do a post-doc in Dr. Mak Saito’s lab. While she’s there, Sara will take her knowledge of diatom transcriptomics and translate it into studying phytoplankton proteomics- making the transition from genes to proteins. But fear not, she plans on continuing to unravel the mysteries of phytoplankton nutrient uptake in her future endeavors.