Saturday, June 30, 2012

Week 4: Flume calibrate and Pressing highlight: Porphyra sp.

Week 4 has ended on a highly positive note.  I spent most of Thursday and Friday afternoon working on calibrating the flume (Friday morning was spent on a lab kayaking trip!).

I built a device called an anemometer, which used glass tubes to measure the amount of pressure caused by fluid motion. I used it to measure the pressure at several points along my base plate.  By knowing how much pressure drops along the base plate, I can directly calculate the amount of shear force that is causing that pressure drop.  And thus I know how much I will be blasting the spores in my tests.

I was so wrapped up in the testing, that I didn't take any pictures of the setup!  But I do have the first data graph to show you.

This shows how the shear force that I'm generating corresponds to the height of the pipe I use in the flume.  The trend is pretty linear, as hoped.  If I fill up a pipe twice as high with water, then twice as much pressure is driving water through my flume, and I get twice as high shear forces in my flume.

And I was able to hit 30 Pa, the magic shear stress number. For whatever reason, most studies haven't been able to go much higher than 30 Pa, so as long as I can get to that force, my flume is working as strong as anyone elses.

I did learn a few things from this testing, such as how the position of my clamps can effect the forces I measure by allowing water to leak out the sides of the flume.  To compensate for this effect, I had to adjust from a four clamp system to a ten clamp system, meaning I had to go buy a bunch of clamps from the hardware store.

Pressing Highlight: Porphyra sp.

This week's algae is probably the most famous of seaweeds. It comes from the genus Porphyra, and is also know as nori, the stuff you wrap around your sushi. It's a red algae, paper thin and quite delicate.  To make nori, Porphyra is ground up, layed flat, and baked into a textured sheet.  You can eat Porphyra (as well as many other algae) raw, but I'll confess it's much improved by the nori processing.

You'll notice that I've left the description at sp. (meaning unidentified species) rather than giving a species epithet. I know there a few Porphyra species in Washington, but I'm not that great at telling them apart. From talking with Porphyra experts at Phycology meetings, I've learned that even the experts are still creating and redefining new species constantly.  So even if I were to use a guide to find the "name" of this species, there'd be a decent chance that name would be wrong anyways.  As a results, I don't bother and just leave most species in this genus as Porphyra sp.

The species I've pressed look a little beat up, almost as if their degrading. But the degrading is perfectly normal for this genus, the red degraded regions are the reproductive parts of the plant.  Porphyra gets reproductive on it edges, converting it's tissue entirely to sperm and eggs.  Once the reproductive tissue is primed and ready, it simple deattaches from the parent plant, to float in the water and find a mate! The reddish color indicates that this is a female, males have white edges.  Some of the red, gooey portions around the plant were egg packets about to be released, and got caught around the edges of the plant in the pressing process. So actually, this individual is quite sexy at the moment, and we quite literally caught it in the act in this pressing!

Thursday, June 28, 2012

Week 4: Testing and tweaking

Halfway through week 4, and moving along.  I solved the last two problems I was worried might trip me up on Monday, making sure the cameras could actually focus on the surface of the glass and weren't too far away, and getting enough light to a microscope immersed in a container of seawater so that I could actually see things underwater.

It's always the little details like this that you don't really think about until the last minute, when you are hooking the webcam into the camera and thinking "So this is going in a tank of water- where's the light coming from?"  And then you hope you're creative enough to find an answer to a problem you didn't realize existed until moments before, but might wreck your whole experiments. So far, I've been lucky/creative enough to not have anything permanently trip me up yet.

I tried a trial test run on Tuesday, where I let an algae release spores and then tried to take pictures of them with the webcam.  It seemed to work, but I never found the spores with the microscope.  They either never were released, got blown off when I assembled the flume, or (most likely) were just too dang small and sparse to find on my giant sheet of glass. I think with a little more care, I should be able to find them, hopeful this won't be the devilish detail that wrecks the whole project.

In any case, here's a picture of my more or less finalized setup:

I made markings to tell where I was on the glass:

And was able to see the marking through the webcam, onto the computer:

Also, this little guy is my favorite example so far of creative troubleshooting.  I was having difficulty finding a way to secure the motor to the metal framing of my setup.  After trying a couple very clean and official techniques, I started getting sloppy and just using zipties to hold it down so I could temporarily use it (and it just so happened the nearest zipties were bright pink).  Finding that worked, I started adding more zipties. And more. And then I laughed maniacally to myself as 8 zipties later I had strapped the motor in every direction I could think of, and by golly it wasn't a pretty solution, but it worked!

Sunday, June 24, 2012

Week 3: Pressing highlight- Microcladia coulteri


Good news, Becca got back on Thursday, we were able to hit the low tide on Friday, and I got some algae pressings done this weekend!  No pictures from the field as it was a pretty crappy, rainy day.  But I wanted to introduce the algae I'll be pressing with short algal vignettes. Hopefully these short stories will give the algae pressings a little more character, and help you appreciate algae the way I do.

There's lots of seaweeds with lots of shapes, sizes, colors, etc., and I'd like as much as possible to be sure everyone who is receiving a pressing as a reward gets one they like. So as the algae pressings dry (which should take about a week), I'll post pictures of the pressings on a separate webpage, where people can claim them on a first-come-first-serve basis.

Week 3 Algal Vignette: Microcladia coulteri

Not all seaweeds are created equal.  Finding the right seaweed for a good pressing can be tricky, some algae that look beautiful in the water just become dull, pasty scraps when pressed. But not Microcladia coulteri: it looks good in the water and on the press.  It has a vibrant red color that dries well, a flattened, two dimensional growth that presses well, and a rugged cell tissue that can be easily spread out without breakage.  It's sort of a classic to me, like Old Spice or Chuck Norris. When I think about pressing algae in the Pacific Northwest, it's the first thing that comes to mind.  So I suppose it is appropriate to have found it on my first trip and to use it in my first pressing.  Microcladia coulteri isn't super abundant on the San Juan Islands, but if you know where to look it is common enough to be easy to find.  So in video game terminology, you might can it an "uncommon drop."

Thursday, June 21, 2012

Week 3: tidying up

Most of the way through week 3 now.  Everything is going smoothly, pretty much on schedule.  I plan to start real experiments come this Monday.

I spent Monday and Tuesday working on coding for the Arduino/webcam setup, and amazingly figured it out.  Check it out, here's the solution I found: I program the arduino to move the motor a set distance, then stop.  I then use the Arduino's built in serial port (genius feature!) to send a signal back to the computer saying "Hey, I'm ready, take a picture!"  Meanwhile, I have a Processing code (new language to me, it's pretty sweet) running on the computer waiting for the Arduino's signal.  Once it gets the all go, it says "Ok boss, picture time," and tells the webcam to take a picture. Slather, rinse, and repeat, for a series of spatially organized pictures of baby spores triggered by the push of one button. Pretty sweet, huh?

Since then, I've been mostly finishing up odds and ends, connecting pieces and cleaning up joints.  Here's some pictures of the flume in a more or less finalized state.

Unfortunately, no field trip this week.  Becca, the grad student who will be working with me on this flume, is currently out of town and delayed in getting back.  She's also my guide to the local algal hotspots, so without her, a field trip is a bit pointless.  Oh well, more on the next low tide.

Friday, June 15, 2012

Week 2: The robot moves!

The last two days were a huge success! I managed to get a fully functioning carriage move back and forth, powered from a stepper motor using a code from an Arduino!  I'd like to say it was my ingenuity that solved my carriage problems, but most of the credit really goes to the lubrication properties of WD40.

This shows the carriage assembly in the coolers that I'll be using for the experiments.

 And, a video of the action:


Unfortunately this drama with the carriage has put me behind schedule a bit.  The flume is nearly assembled, next week will involve assembling the flume, figuring out how to take pictures with a webcam using an arduino, and final programming for the arduino code (not the most exciting or photogenic of activities).  I don't think I'll actually get to calibrating and testing the setup until week 4. 

On the plus side, I've now figured out how to make and bought all of the necessary components for all of the different aspects of this project.  Just in time too, I've nearly reached the end of the budget!

In other news, there's great low tides next week!  I plan on going on collecting field trip, and finding some nice algae to use for the first few algae pressings.

Wednesday, June 13, 2012

Week 2: the flume arises

And week 2 it is!  A lot happening here, the flume is starting to become something recognizable.  Here's a few shots of the pieces I've constructed so far, not much on their own, but they'll look impressive soon.

The base plate, the clamps are holding the glass plate to the plastic sheet until the glue sets.  The spores will settle on the glass.

Moose had some concerns my original design for the connector box being able to supprt the weight of the water and pipes.  So he had the great idea to turn my "box" into a "elbow" (or a 90 degree connector) which solves the problem of the weight support but still leaves me with a circular cross-section of water that need to be rectangular.  To solve that problem, I cut a rectangle out of the pipe cap, and am going to fit a few plastic pieces to form box that reduces the flow to the shape I need for the shear flume.

This is the piece that fits over the base place, and will connect to the connector box. I'm basically just gluing two plastic bars to a sheet of glass.
The biggest holdup so far is the carriage assembly, the thing that the motor moves back and forth.  This has proved both more difficult and more expensive than expected. Right now I plan to use the motor to spin a threaded pipe, with will force a block to move back and forth. But I bought a $50 carriage on McMaster (the key piece of the assembly) that didn't really move smoothly at all, meaning the threaded rod with probably get stuck rather than slip through.  I'm going to make some adjustments tomorrow and try to make this carriage work, but I might need to find another way.

The carriage assembly is also way more costly than I expected.  It seems like each assembly will run over $100, way more than I anticipated (I guessed $20), and even at that price, it's not all that great.  But then I realized that I am completely automating my data collection process, and that this is a pretty awesome and creative way to do it, and when it works it will be so worth it. I had to manually count spores under a microscope as fast as I could in my PhD, and that to avoid that again is worth a little time, energy, and money.  

In any case, it's definitely a good thing that I got more than I asked for initially.  Thanks everyone!  Your generosity has covered my cost underestimate.

Saturday, June 9, 2012

Week 1: motor controls

Wow, eventful first week!  I spent more time than I would have liked getting settled, ordering final parts, and meeting various people, but I still managed to make some progress.

Arduino is ridiculously easy to use!  I sat down with the parts and software on Thursday morning, and by the end of the day, I was able to connect the arduino to the motor and use a code to make the motor spin!  Yay!

Sure, this isn't on the forefront of technology or anything, but it's still pretty damn amazing to me that I can write some random, arbitrary characters on a computer, push a button, and get a motor to do something.

It gets better though, because Moose let me borrow his Arduino LCD shield (a chip that connects to and sits on top of the arduino, giving you a simple display and several buttons).  But the end of Friday, I had programmed a neat little menu into the LCD display that let me control the motor completely through the Arduino.

And that was about it for real progress this week, though honestly, I didn't expect to get a nearly finished code in arduino so quickly, so this is actually more than I expected to get done.

I'm making a page with my current planned schedule, in case you want to follow along and know what's ahead.  Finally, I'll end with a sprinkle of few pictures from the ferry ride here, and the field trip on Wednesday.
Damn, I wouldn't mind living in that house.
Friday Harbor Laboratories, as seen from the ferry as we pull into the port.

Seaweeds! If you're not looking forward to many glamour shots of seaweeds, you're probably on the wrong blog.
A giant Pisaster seastar! And bigger than my hand!  Special exception here due to it's remarkable size, don't expect many pictures of disgusting animals.

Monday, June 4, 2012

Week 1

Ok! All packed and ready to go to Friday Harbor tomorrow morning, via bus, plane, bus, and ferry.  I'm posting this in fear of being one of those annoying bloggers who writes about every little thing that happens ("Now in the Terminal", "Now boarding the plane", "Now exiting the plane!").  Trust me, you'll get none of that.  I am pretty new to this blogging thing though, so if I start doing it wrong, feel free to let me know.

I'll aim for a twice-a-week posting schedule to keep everyone updated, without being overtly annoying. This week, I'm ready to hit the ground running! I'm flying in during a low tide week, so appropriately have some tentative field trips planned for this Wednesday and Thursday with Dr. Patrick Martone, a professor from University of British Columbia and coralline algae expert.  Also, he used to be my labmate and is a good part of the reason I study corallines now. He's one of the two professors I'll be working with this summer.

Friday, June 1, 2012


Special treat today, for all of you eager to see what the hell this contraption looks like.  I sketched out a simple hand-drawn diagram.

As you can see, I'm no artist, but hopefully you get the idea.  There are four pieces, a base on which the spores settle, and then three attached pieces which when added to the base create a shear flume.  Water builds up in the gravity flume, creating pressure.  The water then transfers through the holding box, whose purpose is to connect the vertical 2" pipe to a thin narrow shear channel.  The cover fits over the base, creating a thin narrow opening through which water flows to create shear.

I've now ordered the raw materials to construct each of these components.  Yay! Turns out custom-cut glass isn't so hard to find on the internets, even found a place in Washington to supply the glass pieces, so it shouldn't take them too long to ship to Friday Harbor.