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).
Pretty morning at Santa Catalina Island
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.
Mapping how sound likely propagates through the Southern California Bight in August.My acoustic set up. Sonobuoy detector, sonobuoy recorder, and directions of course.
People started to refer to me as Jonesy. I embraced it whole-heartedly.
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.
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.
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)
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.
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?
Crushing work.
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!
As Niki mentioned in her post earlier this week, Niki, Danielle, and I gave a presentation at Hatfield Marine Science Center this week as part of the Monday Tech Talk Series. On the first Monday of the month, someone from the community shares their knowledge on a new bit of technology they use/feel is important, and the talk is a relaxed discussion type setting so the audience can ask questions and learn more about if that technology would be useful in their work. I’m a big fan of these talks so was happy to be able to give one.
Talking, talking, talking. Thanks Bruce Mate (OSU/MMI) for the photo!!
Our lab signed up to talk about social media, because, we think we are pretty good at it (not a #humblebrag, just an actual #brag)! You are reading our blog aren’t you? And you may have followed a link to it from our Twitter or Facebook page? I wanted to use this week’s blog post to share our presentation and some of the discussion it sparked, for those of you who couldn’t attend (*cough cough* Sharon).
What exactly is social media?
A lot of people think of it as teenagers buried in their phones and computers, taking selfies, tweeting about Alex from Target. But it has become much more than that! The official definition from the reliable source, Wikipedia, is:
“Social media are computer-mediated tools that allow people to create, share or exchange information, ideas, and pictures/videos in virtual communities and networks.”
The point is, social media allows people to share information, over long distances, and very quickly, enabling them to reach lots of different people they may not know directly.
Science – Social Media Connection
That is where science and social media can come together. A huge part of our job as scientists is to communicate our science – to share what we find with colleagues, students, the general public, whoever is interested (or maybe not)! Social media is an outlet to share publications, glimpses into field work, what is happening at conferences, resources that may be helpful, events happening, conservation concerns, I could go on and on. To paraphrase Danielle at the end of our presentation – social media allows people to see scientists as real people, doing cool important stuff, who love what they do, not robots hidden away in a lab somewhere. We get excited about learning, about day-to-day new discoveries, and we have struggles, where things go wrong and we have to start over (or lock our keys in our car).
Types of Social Media
We covered four main types of social media, because those are the four our lab uses, and I posted the corresponding slides below. We wanted to highlight the differences between the different types, because that is the somewhat tricky thing about social media, each outlet serves a different purpose. Each has its pros and cons, and each should be used in a way that best takes advantages of the pros and minimizes the cons.
The audience asked “well which is best?” And I really didn’t have a single answer. Here’s the general consensus:
The website provides an official portal to the lab. Official information, links to all other social media, it comes up when search through OSU and has contact info for the lab. We don’t update it that often. It’s got long term blurbs about people an research.
The blog provides a more personal look into life in the lab. Each of the 5 grad students post once a month (we rotate through) and Danielle posts a fun Soundbites section ever Wednesday. These posts are longer, have pictures, and can be about anything we want…my parents and grandparents follow it to see what I’m actually doing, its sort of like an email to lots of people who care.
Twitter is our quick communication. It keeps us connected with collaborators, colleagues, “fans” (followers) and we have to condense what we want to say into 160 characters, or a picture. We can “retweet” things from other labs we follow, to share exciting papers, or new field work. This is a quick way to connect, but its over the short term.
Facebook is again a more personal way to communicate. It reaches out the same way as twitter in some sense, but posts can be longer, pictures are easier to browse, and we can connect with people through events, and more (see Niki’s post for more detail!!)
Other types of social media exist, such as Instagram, Google+, LinkedIn, and the science-specific ResearchGate. We are less familiar with these so didn’t discuss as much, but they are out there and maybe we will be on them in the future.
Discussion Points
I feel like this blog is getting on a little bit. Describing social media in science could probably be an entire series of posts, but I wanted to just give a brief intro here. I thought I’d wrap up with some of the great discussion questions we got during the presentation (we didn’t get to the end of the slides because of the great interest!!) We don’t have all the answers, but please feel free to ask questions in the comments below and one of us will chime in (that’s the point of this interconnetivity isn’t it??)
How much time should we be spending on this as scientists? Is this taking away from our research?
What about the issue of misrepresentation of your research? (misquotes go misquoted go misquoted)
Where do you start?
Do you think it improves your writing?
What is the value in being able to condense your research to 160 characters? Should that be what we strive for in titles? Should a tweet of your abstract now be included?
Oh, and on a final note…
What the heck is a hastag (#hastag)??
For you scientists out there, think of it like a keyword, the keywords you would put on a paper. By putting the # in front of a word or phrase, it becomes searchable, and then connects your post (on Twitter, Facebook, Instagram, etc) to other posts with the same hashtag.
#SciComm is a great one to start with to tell your followers you are communicating your science!
*Disclaimer: Niki and Danielle, I’m sorry if I didn’t do this post justice… I feel like I didn’t, but it’s hard to describe a discussion in a blog post!! Feel free to augment!!
Well, I took last month off from blogging because I didn’t have much exciting to share. Then my turn came up again this month and again I realized I don’t have much to share. So I decided to go with it and just ramble for a bit. I have been working on wrapping up my master’s thesis and so I’ve been very busy writing, and reading, and writing, and editing, and making Holger read stuff, and writing. But the end is near, I can see the light at the end of the tunnel, all those other catch phrases about finishing something!
This is how I imagine I will feel the morning of my defense.Found inspiration in this guy at the Point Reyes National Seashore.
I spent the Christmas holiday with my family but headed back to Oregon soon after to get back to work. I’ve been fortunate enough to be hanging out on the coast while doing all this hectic finishing up, and it has been surprisingly nice weather. I have been spending a lot of time staring at this screen, but at least the sun has been out my window!! And it makes taking breaks to walk the dog all that much easier.
In the midst of the summer and early fall when I was traveling a bunch and doing field work, I remember thinking how nice the term would be to be in one place for a while and get some analysis/other work done. What I didn’t realize was how unexciting my life would be for blog posts….
I guess excitement depends on your interests, though, because for me there have been SOME exciting moments standing in front of my computer. I’ve spent the last month putting my master’s on hold, instead analyzing acoustic data collected from one of our gliders that was deployed back in March, and then deploying and analyzing another glider all within the month of October. Want to see what I found? Good. I was going to put in the images anyway.
Here’s a Stejneger’s beaked whale click. The top image is a long term spectrogram, or LTSA, that shows 15 minutes. All the little bits around 50 kHz are beaked whale clicks. The middle spectrogram just shows one click during a fraction of a second, and the bottom shows the wave form, or the amplitude of the click.
From the March deployment, the excitement came in the form of TONS of beaked whales. Like so many. Like all the time. Including the super weird looking Stejneger’s beaked whale (Mesoplodon stejnegeri). I can tell the species by what frequency the click is at, how much time there is between clicks (inter click interval, aka ICI fyi), and the duration of the click. They are all unique features for this species of beaked whale, which I know thanks to other people confirming that by combining visual and acoustic data like was done by theses lovely folks at Scripps.
Here’s two porpoise species detected together – harbor porpoise (the two higher frequency red specs) and Dall’s porpoise (the middle, slightly lower frequency). All together a bunch of those clicks make up that light blue section in the LTSA on the top.
The March deployment also brought excitement through porpoise recordings! Did I mention that glider was the first of its kind to record ultra high frequencies? We used a 394 kHz sampling rate, which means we could detect vocalizations up to 196 kHz, which is where porpoise and a few other odontocetes (toothed whales) vocalize. Most equipment doesn’t sample that high (memory gets filled too fast) so this was pretty neat-o. I’m a big fan of looking for these ultra high frequency encounters because they are so obvious in the upper part of the LTSA, far above the background noise.
And like I mentioned, I did go out in the field one day. We deployed one of our new gliders for a few days just outside of Newport in early October, and I went out on the recovery. I took this one super exciting picture of these gulls on the back of the ship. You’re welcome.
Piper helped Holger and Alex prep Will the glider before he got deployed in early October.These gulls agree with “no excitement November”. Until I threw pistachio shells over the side. Sadly this is the only picture I took of the whole glider recovery.
