Grad school isn’t all work….sometimes it means taking off a Friday afternoon and rooting for the home team. Go Beavs!!
more science next time 🙂
Author Archives: selene fregosi
All is NOT calm
Well, this post is LOOONNGGG overdue. But that happens right? It’s still a story worth telling 🙂
I haven’t posted in a while, so lets touch base on the last three months of my grad school life. Michelle mentioned that many in our lab attended the Biennial Meeting for the Society for Marine Mammalogy. It was crazy, but awesome. I gave a talk on my master’s work and was the most nervous I have ever been to give a talk…biggest audience, TWO screens, up on a podium. EEK. I think it went ok though. And the best part of all was that my dad snuck in to watch. And more importantly he refrained from asking a question and embarrassing me.
But that wasn’t even the point of this blog. I just had to brag about my dad coming to my talk because how many grad students get to say that??
Winter Fieldwork
You all know I work on gliders (and here, and here, and here) by now, right? (note to self – write a blog post on HOW exactly gliders work).
Well, I do. And two parts of my PhD are to compare gliders to QUEphone floats, and to work out density estimation from a glider. To do this, we need to fly gliders and floats at the same time, and we need to fly them in a place where we have known locations of animals (which we get from other hydrophones using localization…I’m sure Michelle will talk about this some day soon). Then we can figure out how far away each instrument can hear the animal, and then we do a bunch of stats, and voila! All the world’s problems are solved.
So to get the known locations of animals, we are doing two sets of field work – one using a permanent hydrophone array of bottom-mounted hydrophones called SCORE, owned and operated by the U.S. Navy, and one this summer…more later. These hydrophones were originally setup up, and are still used, for Naval training purposes, but guess what, they also hear whales. Now the M3R program of the Navy Marine Species Monitoring program can use these recordings for studying marine mammals on the training ranges. Anyway, for us to get to use it, we had to do it in the very brief window between Christmas and New Years.
Deployment – Dec 20
Right after the marine mammal conference, I went home to my parents house for a day, then flew down to San Diego, Haru, Alex, and I went out on the deployment, and things went mostly as expected. We were only able to deploy one glider because one had an antenna issue, but we also got two floats out. Yay!
Flight time – All good UNTIL Dec 30 – when we started to have communication issues with the glider…that we COULD NOT RESOLVE. The glider was trying to call the base station, we could see the lights on the modem lighting up, but it could not connect. Come to find out, as phone lines are being updated, sometimes this happens, and there was NOTHING WE COULD DO ABOUT IT. But the glider is still flying we know that, that’s good.
Recovery – Scheduled for Jan 4
Alex and I were slated to fly down from Portland to San Diego, head out early in the morning on the 4th (it takes us about 7 hours by boat to get to where the stuff was), and try to find the glider, that will surface for about 15 mins, every 5 hours, in 12 foot seas, within 2 km of a particular point.
So already, I’m NOT feeling super optimistic about it. Oh and then the offshore weather forecast is bad. Real bad. Like we might get down there, head out of the bay, and have to turn around. I was thinking if we pushed it back we might have a better chance of fixing the communication problem and find a better weather window, but remember, we are working on a typically ACTIVE Navy Range, we have to get our gear out of there before they start training again. So lets go forward as planned.
Wake up Sunday morning, Alex is going to drive from Newport to Corvallis in our rental car, so we can drive to the airport for our midday flight. Guess what. It snowed. Our rental car wouldn’t make it over the coast range. SO. We reschedule our flight for later. Alex gets a ride over the hill from Haru, who has a truck. We take my Subaru to the airport. WORST DRIVE EVER. Corvallis snow melted, Portland was in a full on ice storm. Cars sliding off the road everywhere, somehow we make it (Thank you Remy Lebeau…my car).
Oh but wait, halfway there, I get a text message that our flight has been cancelled. Alaska automatically re-routes me: Portland to LA, LA to Seattle, Seattle to San Diego..midday on the 4th. REMEMBER we need to get our stuff on the 4th. The weather forecast has gotten worse for later in the week…Monday is our only chance. Oh and bonus, Alex got rerouted as well…for Tuesday the 5th, at 7pm, direct flight Portland to San Diego. SUPER GREAT!
But don’t worry, I’ve got a plan. We fly to LA, just to LA, we rent a car there, we drive the two hours to San Diego, its all good. Granted, the LA flight is from 8-10, so we would get down to San Diego by about 1 am, but we would make it to the boat for our scheduled departure at 4. So ok…lets do it.
So we call Alaska, and we wait on hold, while driving through ice, for like 45 minutes. Finally we get through to this very nice woman, who fixes everything (oh and we have to run all our travel through our accounting people too, on a Sunday night, so there are lots of calls being made). Alex and I, both on the flight to LA. Great.
We get to Portland, we park, we check in for our flights, we go to Enterprise to switch our car reservation to LA. We wait. Guess what…LA flight is delayed. Yup. Ok, we board, only an hour late. Then we sit. On the tarmac, while the de-ice the plane. Yup. I’m a west coast girl, born and raised….this is all so weird to me!!!!!!
So we make it to LA. Midnight. We sit. On the runway. For an hour. Because our gate had an oil leak. YUP. ok…we get off. its 1:00. Remember, we are supposed to be at the base at 3:30, to meet our escort to the boat at 4. It takes 2 hours to drive from LA to San Diego. So we’ve got 2.5 hours. WE MIGHT MAKE IT!!!
The enterprise shuttle is late. Its supposed to come every 10 mins, its too far to walk (45 mins, we mapped it). It comes…1:30. We get to Enterprise. WE SPRINT OFF THE BUS to beat everyone else on it (it was very crowded because we weren’t the only travelers with issues).
We get our car. its 1:45. We start driving. Thankfully I used to live in Southern California so at least I know where we are going. Plus Alex helps me navigate. We text the boat crew…we will be a little late. Forget checking in to our hotel, we are going straight to the base. YAY WE MAKE IT TO THE BASE AT 3:45!! Did I mention its raining now, and again the glider isn’t really communicating so we will be finding a needle in a hay-stack of waves. But we actually made it to San Diego.
Then we sleep. The AMAZING crew had our beds all made 🙂
—took a break from writing this blog post to get free cake—
Ok, so we sleep, for a while, till like 7 or 8, then my phone starts beeping. The crew says we are getting close. We discuss where exactly we are heading. We are super far offshore BUT we have this super cool satellite phone wi-fi hub thing that can forward sat phone texts and calls to my regular phone wherever I am on the boat (WHAAAATTT). Haru is giving me up dated info on the floats. AND. WHAT. MIRACLE. THE GLIDER CALLED IN. Oh side note, it is super rough and I’m looking at computer screens at this point and repeating over and over in my head “dont throw up dont throw up dont throw up”.
So now we’ve got a glider location, but we are a couple miles away and we don’t know how long it will stay at the surface. I go to lay down for a few minutes while we move towards it. The captain comes into the server room where are temporary bunks are. “Uh….I think I see it…”
I jump up. Run outside. There it is, sitting in a kelp patty. Just sitting there. I suddenly do not feel sick. I hug the boat captain (I can’t help it).
Then the fun begins, because its so rough and we are on a pretty big ship we deploy a little RHIB (all black, Navy style) off the back of the boat and go out to pick it up.
The rest is somewhat less memorable. The floats were easy to find, the sun came out and I lay on the back deck soaking it up, the crew made dinner, we drove in, got to the hotel at 8 am the next morning, had a mimosa, slept, packed everything the next day, and flew home.
The end.
This turned out a lot longer than I anticipated, and perhaps the stress and anxiety and then happiness did not come through this…but writing about it brought back some heart racing…so trust me…it was stressful. But it all worked out. Yippee!! Now I can’t wait to look at these data and actually do something with it.
Plus..serious shout out to Alex, hes glider tech/pilot/friend I could have out there.
Forward Progress
So….Guess what? I figured out my dissertation!
Well, not really. Not the whole thing. But I finally feel like I have sort of the start of an idea of a plan. Yesterday I gave a talk at the Marine Mammal Institute Brownbag series at Hatfield Marine Science Center. I took this opportunity to try and sketch out what I will be focusing on the next few years.
I got some great feedback that will really help me going forward. For example:
The problems you discuss seem similar to problems that were worked out for visual surveys in the past. That would be a great place to start in your literature search.
Great point! That’s kind of what I was trying to convey…so yay!
Well. If I’ve got one thing to say. It’s a lot.
Again…I agree. I hadn’t realized how big it all seemed until I got it all out there. But it’s a highly collaborative project, so I think it will be doable? And I’m sure things will get tweaked. But I do need to be reasonable here.
You really nerded out up there.
Heck yes I did! Gliders! Woo!
**I paraphrased all of these so I won’t put the names of who they were from 🙂 I think I got the gist of what they meant?
Call me Jonesy
Wow! Summer winded down quickly. It felt like a lot of time spent writing, some exciting and stressful glider piloting, and I wrapped it up with 2 weeks on the water in Southern California working on the SOCAL BRS project. (You can read a public summary of the project here).
I’ve talked about this project before, and this was my 4th summer on the R/V Truth. This leg ended up a bit frustrating in the fact that the animals were more difficult to find and work with than past years. We didn’t observe the distribution of whales we typically do, and we suspect this has something to do with the abnormally warm waters off Southern California this summer.
For example we barely saw any Risso’s dolphins, where typically there are tons around Santa Catalina Island. And the blue and fin whales typically found feeding right in the LA shipping channel weren’t where we expected them. Instead we found them quite a bit further offshore near Santa Barbara Island. AND we saw schools on schools on schools of yellowfin!! (I think……I may edit this in a day or two…anyway I’d never seen so many leaping fish!) EDIT: Yellowfin tun and maybe some small bonitos and maybe some bluefin.
Always Learning
For me the trip was still a great learning experience. I got to use some new tools and learn some new skills, including running the sound propagation software we use in setting up a CEE (Controlled Exposure Experiment), running the sound source that projects the sound playback, and deploying and recording from sonobuoys, little one-time use floating recorders designed to listen for subs, but also work for whales.
Reporting for Duty
I’m going to take a page out of Danielle’s blog/book this week…and talk about thinking.
About one year and 3 weeks ago, Danielle touched on the value of taking time to just think. Not day-dreaming just thinking about all of the Patagonia jackets I want to buy, but thinking about my project, my science, what….and why…I’m actually doing…and doing it.
Since I defended my Master’s in May, life has been a whirlwind. I had a few travel plans for the summer (a conference in July and some field work coming up in a week), there were gliders to be piloted (in Newport and the Gulf of Mexico), I needed to finish up my manuscript of my master’s research and submit it (still in progress…), and there were reports – oh reports – to be written.
Every time I come to blog I can’t remember how much I’ve talked about what my PhD will be about. I feel like I haven’t really, because I don’t even know that well yet! (That is where this whole idea of thinking comes in right now)
The basics, though, are that I’m part of a large scale monitoring project involving flying gliders outfitted with passive acoustic recorders in several different naval training ranges around the Pacific. All of these glider flights are funded NAVFAC, aka the operational U.S. Navy. They want to know what cetaceans are in the areas the use, and when. We have to answer their basic monitoring questions, and then I will get to use this HUGE dataset to do something for my PhD. But first, we have to answer those questions. And that is done in the form of a report. The thing about these reports are that they have deadlines. Very strict deadlines. And they are all stacked on top of each other. So since May it was – analyze MIRC, submit MIRC draft, get MIRC draft edits, revise MIRC draft, submit MIRC draft to Navy, get Navy edits back, submit MIRC final. Then lets put in the exact same thing for HRC (Hawaii) and go over it again:
Analyze MIRC, submit MIRC draft, analyze HRC, get MIRC edits, revise MIRC, submit HRC draft, submit MIRC draft to Navy, get HRC edits, revise HRC draft, get MIRC edits, submit HRC draft to Navy, revise MIRC, submit MIRC final, get HRC edits back – ok – this is where we are at…..now waiting a bit…oh and the Washington and Alaska and other Hawaii reports are do mid September and October and November.
All this happened in a matter of 3 months. That may seem like a lot of time, but please remember all the other stuff going on. Anyway, I’m losing focus here, the point of all of this is that since finishing my Master’s and shifting my focus to my PhD, I haven’t had a chance to stop and THINK. And that is what I’m tasking myself with for the next little while. It’s easy to get caught up in the “putting out fires” way of working. One deadline to the next. But I have to stop right now and think about what I am actually doing. I am a graduate student. I’m learning to be a scientist. And I need to spend some time coming up with the questions that will ultimately make up my dissertation.
So with that, I am ending this blog as the stream of conscious that it is. And there are no pictures. And I’m sorry.
Busy times call for….
links to other blogs!! Like this one: LADC-GEMM
Lately I’ve been doing some “field work” although that is not nearly as glamorous as my labmates Michelle and Samara are doing right now. I am piloting a glider in the Gulf of Mexico for a monitoring project around the area of the 2010 Deepwater Horizon oil spill. This is an awesome project because it is using three types of passive acoustic monitoring systems: gliders, autonomous surface vehicles (that look AWESOME) and bottom moored hydrophones. However, me piloting means staying in Oregon with a strong internet connection and doing all of that from my laptop, so I don’t have any cool pictures, or fun field stories. This deployment has been going very smoothly, compared to the test flight, knock on wood.
Anyway, Sara Heimlich, of the OSU/CIMRS Bioacoustics Lab, has been maintaining a great project website and I encourage you all to check that out for more detailed info…and cool field photos.
Enjoy!!
Miracle (2015): A lesson in waiting. And teamwork.
I feel like I experienced a miracle last week.
Possibly I am throwing around the word “miracle” because I’ve got Herb Brooks on my mind (thanks to my fellow grad student and FW intramural soccer coach Matt who is obsessed with that guy). Or perhaps that is actually what happened.
Let me set the stage. Will and Otis, our two Seagliders, were deployed off the coast of Newport, for what should have been a brief, straightforward test of their passive acoustic systems before they were shipped off to the Gulf of Mexico for a project there. Of course, that would not be as exciting of a story if it all went as planned.
I can’t remember how much I’ve talked about it before (I looked it up…try here and here), but basically, the way these gliders work is they go out and dive in the ocean, listen for marine mammals, and every time they surface they call in to a basestation, offload their location and some log files, and continue on their way. Well. Otis (SG608) did exactly that. It was his first flight with us and all went smoothly, from a piloting stand point. Will (SG607) on the other hand….well, he went rogue. And I don’t mean to the brewery.
Will stopped calling in after only 5 dives. Did I tell you this was my first “solo” piloting of the gliders? Yes, I was sort of freaking out.
But what happened the next few days is not important (I blacked it out so I can’t tell you because I don’t remember).
The point is….WE FOUND HIM!!!!!!!!!!
So (1) the miracle part: Let me explain the chances of finding Will. Best case scenario we were searching in about a 1 km radius of a point we THOUGHT the glider would be diving to. Worst case, it was floating at the surface and had drifted who-knows how many miles offshore. But lets complicate things. Glider at the surface, great, easier to spot. Glider continuously diving = glider down for 1 hour 40 mins, at the surface for 20 mins. So lets say we ARE in the right place. Well then it has to be the right time, and you better spot the thing during that 20 mins and get the boat over there before it goes back down for an hour and 40 mins and pops up somewhere else in that 1 km radius. Lets add in some wind waves (We are 35 nm offshore here) and some fog. And this is the image you are looking for:
(2) the waiting part. Will was missing for 4 and a half days. That doesn’t seem like that long. But when everytime your phone beeps that you get a text message and your heart jumps thinking maybe its the glider, that is a long 108 hours. But that is a lot of what we had to do. This was exacerbated for me because I had to stay on land during the search trips. I had to be at my computer in case we heard from the glider and I could give updates on GPS locations or timing. This was a new experience for me. I’m not real good at sitting still and waiting.
(3) the teamwork part. To me, the greatest outcome of the whole thing. There is NO way we could have found Will without all hands on deck, without awesome grad students and scientists who went out to look (Laurie, Niki, Erin, Theresa, Curtis, Alex, Haru, Matt, Dave), Anatoli and Steve for answering my piloting questions, a chartered fishing boat (ok…we paid them, Sara thanks for coordinating), TWO trips out, the people at iridium for putting up with my incessant phone calls, the dolphins that swam by the boat and provided moral support, Sharon and Holger for telling me not to freak out…I could go on. (and I’m SO SORRY if I am forgetting someone)
Jack of all trades, master of one
So…it was my week to blog. I’m a day late. That’s because I was sort of busy yesterday. Defending my master’s thesis (this stuff). I passed!!
So I’ll leave you with this photo of me attempting to relax after a somewhat nerve-wrecking day. Now on to publishing the results!
Note to Selene: The Earth is Round
Today’s blog serves two purposes: (1) inform readers what’s going on in my research world and (2) an educational piece sharing some of my trials and tribulations with ArcGIS this week.
Right now we are preparing to deploy a glider up in the Gulf of Alaska, near Homer, in the US Navy’s Gulf of Alaska Temporary Maritime Activities Area. The glider’s acoustic system samples at 194 kHz allowing us to listen for vocalizations up to 97 kHz, which covers almost all cetacean species in the area, except porpoises which vocalize at really high frequencies (>150 kHz, we recorded them with a different glider though!).
I won’t be actually going out to deploy it or piloting this glider – we are collaborating with some folks from the University of Washington – but I am responsible for putting together the glider’s track and coming up with track points that are 5 km apart so we can set our ideal path for the glider. Why am I responsible for this, you ask? Well because I took an introductory GIS (Geographic Information System) course so….this becomes my job.
For those of you that have worked with GIS, you understand there is a STEEP learning curve. It may be one of the least intuitive programs on the planet. But, it is incredibly powerful for not only making maps but for spatial analyses too, so I am super happy to have learned even a tiny bit about it and get to learn more every week.
Well I’ve made these maps before for Guam and Hawaii, so Gulf of Alaska, easy peasy! I’m finally starting to remember how to make the track from the initial way points, then turning the track into 5 km spaced points. But, news flash! The earth is round. And measuring things at higher latitudes gets weird/complicated/annoying/inaccurate/etc.
So this week (really the last two days) I taught myself about projections in ArcGIS. Projections are basically trying to show our round, 3D Earth in 2D. At the equator this isn’t so bad, but up (and down) by the poles things can become really distorted.
Take this image of the US for example. Depending on what projection you use, it looks slightly different! And those differences are more pronounced the further north you get. So by the time you get to Alaska…well, you’ve got to do something about it.
Fortunately, lots of people have made hundreds of projections for different areas and different spatial scales that reduce distortion, either in area, distance, angles, etc.
So then all I had to do was find the one I needed (this took much research and trial and error), then redo all my mapping/measuring/GPS coordinate extracting steps on a correctly projected map. You know, once you make sure all parts of your map are in the same projection, that the data frame has the right projection, and that you saved it every 5 seconds in case it crashed. Once I got past the frustration, I ended up pretty proud of myself, and now I learned my lesson for next time: only work in areas near the equator.
Want to know what projection I used? Of course you do. The lovely Alaska Albers Equal Area Conic! Sorry I can’t share a picture of the pretty map…I’m not sure I should show you where our glider will be I don’t want anyone going up to Alaska and stealing it.
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Power Stance
This blog post has NOTHING to do with bioacoustics. Or noise. Or marine mammals. Or even terrestrial mammals (ok, well technically humans). This blog post is about the awesome-ness that is my stand up desk. A lot of folks have been asking me about it lately so I figured, why not share the joy?
I’ve had my stand up desk for about a year now, made from this IKEA hack for about 22 bucks. I am proud to say no less than 5 of my closest friends and colleagues have since also made themselves some version of this (I’m so hipster, its the Oregon way). Many grad students in life science, ecology, marine science, wildlife-y fields pursed such a career path because they love being active, being outside, etc. Look at any of the bio’s of ORCAA students, for example. But what do we actually do most of the time? Sit at our computer.
I have far too much energy to just sit at a computer all day!
So now I’ve got this sweet set up. Not only do I stand at my desk, but I just added a balance pad for EXTRA muscle engagement. I can’t take credit for this, fellow grad student Thaddaeus Buser passed on his balance pad obsession/wisdom to me. And now I pass it to you.
Questions I gotten asked include:
Don’t you get tired all day?
Yes…at first it was really hard! But it gets easier.
What if you want to sit?
Well I don’t have one of those fancy up and down desks or a nice tall chair (that is what dreams are made of), so I take my laptop or some reading material to the library, or a coffee shop, or wherever. It gives me a change of scenery (which I like) plus a little rest.
Is it distracting?
Nope. I actually find it much easier to focus because all my pent up physical energy an outlet now.
I will admit certain work activities are easier sitting (writing) vs standing (Matlabbing), but again, that’s what all the little work spaces around campus are for!