June 2010 Archives

Where's Sheldon? The plankton-or-detritus game.

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We live in a digital age.  Grocery stores use automatic scanning to read prices.  Factories use machines to build machines.  Robots can vacuum carpets and land on Mars.  Even our trusted local RoboCop struggles with his dual cyborg identity.

But what does this have to do with plankton?

Digital instruments are changing the way we view the ocean as well.  While nets are still the most common plankton sampling device, other instruments are starting to catch on.  In our lab, we use the laser optical plankton counter, or LOPC, which I've written about before.  Instead of hauling up a net and counting every critter by eye, we lower this instrument into the ocean, it scans the nearby water with a laser, and records what it sees.  Very futuristic.

The advantage to this technology is that we can now collect large amounts of detailed data at a much faster rate, and sometimes in rougher weather conditions.  Also, we don't have to mess with chemicals and look through a microscope for long hours to identify each critter one at a time.

Still, as we march relentlessly toward a dystopian future ruled by hyper-intelligent robots, it's important to bear in mind the value of a human--in this case, a taxonomist human.  To illustrate the point, I've invented a game called "Where's Sheldon?  The plankton-or-detritus game."  When we lower the LOPC into the water, it records every particle that is sees.  Some of those particles are planktonic, and others are not.  It can often be difficult to distinguish the two.

Can you tell the difference?  I did a lab test, and passed these items through the LOPC:
Thumbnail image for LOPC_items02.jpg
As you can see, there is one planktonic organism--Sheldon the copepod--and a collection of detritus.  Each item passed through the LOPC three times.  Here's the output:
Can you identify Sheldon the copepod?  Click on the figure for the answer.

Some of the items are easy to identify, like the coin and the paper clip.  Others are trickier.  Also, these items are roughly 10 times larger (at least) than the plankton that we're interested in.  Now imagine not just trying to pick out the plankton, but trying to identify the species.  That means that the plankton-or-detritus game that we play in the lab is much more difficult than the version that you just played.

To me, this is an important reminder of the value of expert humans.  It's also a reminder of the value of collecting samples of actual animals that can be identified by eye.  Digital technology, so far at least, is at best a good compliment to conventional methods.

On the other hand, in order to get around this problem, scientists are now using machine-learning algorithms.  Essentially, this means that we program computers to be able to think, and they are definitely getting smarter and smarter all the time.  Still, I think it'll be quite some time before we have robot oceanographers.

Feeling the pressure...

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I've been trying to write this last entry for a few days now, but we've been having real fun trying to get the internet! Something to do with the satellite being on the equator, and us being in the Arctic...

So we're over a week in to the cruise now, and everyone has settled in to somewhat of a routine. However, once in a while, something comes up that throws us all for a loop. A couple of days ago was my turn.

Part of my position here is to deploy sediment traps, and another is to run the experiment for primary productivity. This second one involves me getting up before sunrise and "spiking" samples with a radioactive carbon isotope. The samples then sit in an incubator for 24 hours
photosynthesising, and I get to filter them after that.

Arctic blog 2a.jpgPutting the samples in the deckboard incubator.

The idea is that we can use the C14 isotope to see how much carbon the phytoplankton are creating each day. Normally I get to do this experiment every other day - set it up one day, take it down the next. BUT! If we have to deploy our sediment traps, we MUST do a production experiment. That means that occasionally I double up, and a couple of days ago I had to do exactly that.


Arctic blog 2b.jpgRecovering the sediment trap array

Two productivity experiments and a sediment trap deployment and recovery meant that I only got 2 hours of sleep over a 42 hour block. Sleep deprived, I finally managed to take a break when we reached the first deep site of the cruise. This station, one of two that are greater than 2,500m took over 4 hours for us to profile with the CTD. It also meant that we could cover the CTD with styrofoam cups.

It's somewhat of a tradition that oceanographers have. One deep station per cruise is unofficially designated as a cup cast, where all the scientists on board decorate cups and tie them to the CTD. Now, styrofoam is mainly air, and as the pressure increases with depth, the air gets forced out of the foam and the cup reduces in size. This particular cast was to a depth 2,700m (8,900 feet, or about 1.8 miles). You can see from the picture below how much the cups shrink - they were both the same size before the cast! Just to give you an idea of the pressures involves, at the bottom of the cast, there is the equivalent pressure of 270
atmospheres, or over 4,000 pounds on each square inch!

Arctic blog 2c.jpgStyrofoam cups, before and after a trip to 2,700m

We've deployed traps again today, and they are due out tomorrow. Looks like I've got
another block of no sleep, so the bunk is looking very tempting right now. G'night


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One of water's great features is its ability to absorb many kinds of radiation.  For example, ultraviolet light, the kind of light that gives your a sunburn and tries really hard to destroy your DNA, can only penetrate a few centimeters below the ocean's surface.  Visible light fares better than UV, but visibility in clear water is limited to only about 100m.  While water's ability to absorb radiation allowed life to evolve on our planet (thanks water!), it also means that mammals like us who rely on visual cues are limited in the water.

Because water is much denser than air, water is very good at transmitting sound, especially at low frequencies.  This is why whales, which evolved from land-dwelling ancestors, evolved a remarkable ability to make and interpret sounds.  Through a long, convoluted process, our lab is leading the marine mammal monitoring work for UMaine's offshore wind project.  Because of the role that sounds play in the lives of whales, one of our main tasks will be to monitor the sounds emitted by the wind turbine and calculate the acoustic "footprint" of the turbine.  

We have purchased a special microphone, called a hydrophone, that is designed to be used in the water and have been making some recordings of sounds here in Portland Harbor.  Although our neighbors might disagree, one of the most interesting sounds in the harbor this summer is the sound of the pile driver being used to build GMRI's bulkhead (time lapse photos here).  Earlier today, Pete and I went down to the dock next door and made some recordings before and during a pile driving session. Before the pile driver started, the harbor was fairly quiet, other than some grinding being done on a boat next to us. Here's what is sounded like: test3_background.wav.  And, here's what the sound looked like:

This kind of visualization is called a spectrogram.  It shows the intensity (indicated by the colors) of the sound at different frequencies (vertical axis) and at different times (horizontal axis).  The intense green band shows that the grinding sound is strongest at about 0.55 kHz (550 Hz) and that the sound has regular overtones at higher frequencies.

Now, here is the pile driving: test3_pile_operating.wav
You'll notice that the sound is much louder and is concentrated at the very lowest frequencies.  The intensity decays continuously to higher frequencies and also decays after each strike.  It's hard to hear, but each strike produces an echo (small green blobs at the bottom, for example, just before the 6s mark).  Because lower frequencies transmit better through the water, the echo only appears at the lowest frequencies.  Similarly, the sound we recorded in the water is much lower frequency than the sounds our ears heard.  Here's Pete's iPhone video:
and here's the corresponding spectrogram:
There's clearly more sound at higher frequencies; however, the lack of signal at the lowest frequencies is most likely due to the iPhone's microphone "rolling off" at these lowest frequencies.

Just thought I'd post a quick update, and share a few links with you. The first is a ship tracker. It gets updated every so often, so the position may be a few days out of date. You can check out where we are by looking at this site.

There's also several other people blogging on here too. We have a school teacher from Rhode Island, who is shadowing our lab group, and a journalist who is writing for Nature magazine. Hopefully I'll finally get my name in Nature! Finally, the official site will have updates from the Chief Scientist, as well as all the details about the other five Bering Ecosystem Study (BESt) cruises that there have been. It's not been published yet, but we have been told that the first post has been submitted!

I'll post again tomorrow, as we will be deploying sediment traps - basically several open topped tubes that catch anything and everything falling in to them. I'll explain why after we deploy them.

EML goes Arctic!

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My last post was all about the distances that I'd travelled being an oceanographer.
Well, I've now left the lab in Maine, and I'm on a research cruise in the Bering
Sea. We left Dutch Harbor (of Deadliest Catch fame) on the 16th July, and we'll be
out here for a month. Dutch is very much like Portland - a working waterfront, heavy
on the fishing. The big difference, apart from the cold, is that they don't really
have any seagulls. They have things a lot bigger...

Arctic blog 1.jpgI'll post later with some details about what the hell I'm doing up here, and also to
put more cool pictures up.

Well, I thought that I could get away with it, but I was wrong. I've been here since the end of March, and I've avoided writing in the EML blog. Not intentionally, I hasten to add... well, maybe a bit. Doesn't mean I haven't been reading it though!

I've been here on a short term contract, working on the sea surface photogrammetry project. But it's not the project that I decided to write about. Based on a comment made by Andy in my presentation yesterday, I wanted to write a bit more about the size of oceans. Andy (here) and Pete (here) both recently wrote about sizes, and what they compared to, so I figured that I'd join in.

I've been lucky enough to travel to most corners of the world for my work. I started in Bangor (North Wales, not Maine) where I did my undergrad, and then headed to Dunedin, New Zealand for my Masters. Total separation: 11889 miles, or in keeping with weird comparative measurements from previous posts, 382662 Olympic Swimming Pools (OSPs), 174369 American Football Fields (AFFs), or my favourite, 1.12415 x 10^7 Smoots, plus or minus one ear. If you think that is the longest distance travelled by an oceanographer, keep reading!

After New Zealand, I headed to Bermuda (a mere 9411 miles, 302902 OSPs, 138024 AFFs, or 8.89842 x 10^6 Smoots) where I worked on the BATS project for several years. That's the Bermuda Atlantic Time-series Study. Nothing to do with flying, squeaking furry mammals. That was a multi-disciplinary project that studied the full ocean depth just off Bermuda. Full ocean depth was 4200m, or 2 and a bit miles, or half the height of Mt Everest. The project had run for over 20 years, and in that time the various ships had travelled the equivalent distance of once round the world at the equator, or about 25,500 miles!

The coolest thing about studying there was when I found out that water can be given an age depending on its depth. At 4200m, the water hasn't been on the surface for nearly 1000 years! It just gives you an idea of how much information the deep ocean can give us. BATS was only one point in the ocean. We actually know more about the far side of the moon than we know about the deep ocean.

Anyway, enough digressing to small distances. Not satisfied with 3 continents, I moved on to my fourth. I worked for a year in Brazil, which was 4046 miles, 130219 OSPs, 59337 AFFs or 3.82547 x 10^6 Smoots from Bermuda. The work there was for an oil company, and we used scientific equipment to look at currents and density changes, helping to plan the locations of pipelines. Not quite as deep as BATS; we only studied to 2200m.

Staying with oil, but moving to just the surface, I came to the EMLab at GMRI (4916 miles, 158238 OSPs, 72105 AFFs, or 4.64860 x 10^6 Smoots), which brings us back to the beginning of the blog post. There's still one more step for me though. I leave here tomorrow, 11 June, and I'll be heading cross country to Alaska to start my Ph.D. I've got a 12 day drive to look forward to, where I'll be covering at least 103072 OSPs, 46967 AFFs, 3.02798 x 10^6 Smoots, or in plain English, about 3202 miles as the crow flies.

I got in to oceanography for the chance to travel. In the ten years since I started at University, I've been to 4 continents and travelled the equivalent distance of 1.1 million Olympic swimming pools, nearly half a million American Football Fields, or 31.6 million times the height of poor Oliver Smoot. Hm? In English? I've gone about 33,500 miles in ten years, which is half as much again as the BATS ships managed in 20 years.

Become an oceanographer. See the world. No really, you will.

The Smoot - http://en.wikipedia.org/wiki/Smoot

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