Fotos of fog.

A few photos of last week here in Charleston/Coos Bay.



Fog off of Cape Arrago. It's been like this most of the week.

Another fog shot. You can't see them, but there are pinnipeds all over the rocks making quite a racket!

Foggy daze in Charleston, OR

Change is in the air here at OIMB. Most of the students have finished their classes and are now packing up for their moves back to Eugene or whichever part of the country they came from. A handful that are taking an intro stats class remain, but campus has quieted down significantly. Despite not being in class with them, I got to know most of them pretty well, and it’s been a pleasure spending the summer with a great bunch of up-and-coming marine scientists.

Due to fog and unfriendly seas, the urchin surveys didn’t happen last week. It was also a short week due to a mandatory furlough day for ODFW on Friday. Much of my time was thus spent assembling my Power Point presentation and measuring a few samples of pink shrimp that came in. The toughest part of my presentation is definitely the results section. I feel like I pretty much have the interpretation down, but the organization as far as slide order and how to tie it all together for effective communication is a bit tricky. Scott has, of course, been great with helping me to fine-tune it and in providing constructive criticism, but it’s ultimately up to me to finalize it and present it effectively. Oddly enough, the final “thank you” slide is also posing a bit of a challenge. The list of people to include is quite long, and as I whittle it down to be more manageable I feel a tinge of guilt as I remove names and relegate them to the “thanks to everybody else” category. These things must sometime happen. Other than that, I’m very happy with the way my presentation has come together. I look forward to the symposium this Friday with a little nervousness but mostly optimism and high hopes.

My last week here in Charleston may or may not involve sea urchin surveys. As with the previous week, it’s all weather dependent. So far the forecast is for more fog, so I’m not getting my hopes up. It would be so nice to finish up with some fieldwork, though. The last two weeks have largely been spent in the lab or in front of the computer, which I’ve learned is not my favorite place to be despite the satisfaction of seeing the results of my project and gaining much-needed software skills. There’s been talk among the remaining students here of having a bonfire on the beach tonight, so maybe I’ll do some sort of ritual to stave off the fog and reel in some sun.

I bid you peace.

Sea Grant Blog, Earthdate 0812.2012

Another week of my summer Sea Grant experience has passed; I’ve reached the point where the conclusion of my internship with ODFW is in sight. I have mixed feelings of melancholy and excitement regarding this. On one hand, this has been an extraordinary experience that I’ll miss. Living on the Oregon coast, especially in a semi-isolated town like Charleston, has been like living in a different world. It’s difficult to describe, but there’s definitely an underlying subculture here that’s unlike any other I’ve previously experienced. The connection to the ocean and the importance of its resources permeates everything here. It’s one of several things I’ll miss. On the other hand, though, I look forward to sleeping in my own bed again and cooking my own meals (though the food here in the OIMB dining hall has been stellar). I look forward to the warmth and sunshine of Corvallis (it struggles to reach 65 here and is often foggy/overcast) and to being on campus at OSU once again. I know I will emerge from this experience as a changed person, and I wonder what it will feel like in a month when I look back on it all.

Speaking of looking back, I spent more time last week in front of the computer running stats, generating maps, and starting on my final presentation. The statistics are yielding some interesting differences in cockles between the two survey sites. This is encouraging, because one site is within a reserve where the taking of clams is prohibited, and another site is outside the reserve where clams are harvested at least semi-regularly, so we would expect to see some differences in the data. We’re going to have a closer look at the characteristics of the data (normality and equal variance) to determine if parametric stat tests will be reliable. So far we’ve been using non-parametrics, based mainly on suggestions made by the stats software. However, parametric tests can be more powerful when all the underlying assumptions are met, and we don’t want to rely completely on the software to guide our decisions. Furthermore, some of the non-parametric test results seem to contradict each other, and we’re not sure why. It would take too much writing for me to explain it here, but suffice to say the results, despite being interesting and encouraging, have still prompted us to examine the data a bit more and assess our stat methods.

Data analysis has been one of the biggest challenges for me in the past weeks, especially when it comes to analyzing graphs. I’ll take a look at a graph and am able to interpret what it’s saying, but applying the interpretation to the bigger picture with respect to cockle population dynamics and providing answers to questions about “why this” and “how come that” is more challenging. I think it probably has something to do with my lack of in-depth knowledge about the biology of shellfish and the fishery industry that harvests them. I’ve thus been digging into past research in an attempt to gain deeper understanding of cockle population dynamics.

Last Thursday I stopped by the office of Jamie Doyle who is the Sea Grant outreach representative at OIMB. We had a nice conversation about what I’ve been doing over the summer, my interests, and future plans. We talked some about Oregon Sea Grant and the role she plays and future opportunities. It was good to have the chat.

I’ll be helping out with some red sea urchin surveys this week, which I think may involve going out on a fishing vessel. It may be dependent on the weather. We’ve been getting a lot of fog lately, and visibility has been zero. Thus for safety reasons we may not be going out. Hopefully the weather will cooperate. It would be nice to get out into the field one last time before my internship concludes. We’ll see. I will be spending additional time this week dialing in the stats for the cockle surveys and working on my final presentation.

Keep your eyes open, I may have more photos to share as well.

New survey site, habitat data, and muddy mishap

 Last week we journeyed once again into the South Slough of Coos Bay for another Cockle sampling. This time we went to Valino Island, which represents a more heterogeneous habitat than our previous survey at Indian Point. That is, the substrate at Valino Island ranges from a softer, muddier consistency to a firmer, sandier consistency whereas Indian Point is more consistently sandy. Much of Valino Island is muddy, so the raking and walking were a bit more arduous. There was also considerably more eel grass at Valino, so we wanted to take some extra care to minimize our impact on it. Nonetheless, we managed to rake up around 120 cockles, which I measured, weighed, and put into the database. The cockles seem to be less abundant in the muddy areas with eel grass and more abundant in sandier areas closer to water sources like channels and pools. We’ve thus decided to expand the study to include habitat as a factor for cockle distribution. Since we didn’t take habitat info down in our initial surveys, we took some extra time and revisited each quadrat at each site and recorded various habitat aspects: substrate type (sand, mud, smud [sand+mud]), presence/absence of eel grass, presence/absence of gaper clams. (note: for a more detailed description of our field methods, see blog entry for 7-23-2012). In my last blog entry I mentioned starting in on some stat analyses. Due to last week’s fieldwork, we weren’t able to start much in-depth interpretation, but we did decide to collect some extra cockles at each field site to boost our sample size. We randomly selected approx 20 quadrats at each site and raked up about 70 extra cockles per site. This should help beef up our data for further analyses. So far it looks like nonparametric hypothesis tests are the way to go, because our sample sizes aren’t large enough to assume a normal distribution. Something I’ve learned through these initial stat analyses is that our sample sizes need to be very large in order for standard parametric tests (T-test, ANOVA, etc) to be valid. This morning we journeyed back to Valino Island to collect habitat data and more cockles. My confidence for walking on soft mud has increased—to a fault: at one point I let my guard down, my foot got stuck, and I fell right on my backside in the mud. Luckily my chest waders saved me from total disaster. Nothing hurt but my pride, and I may have an interesting photo to share. The rest of the week I’ll be generating pivot tables, which are very helpful/powerful when looking at data (more about those later when I learn more) and doing some more in-depth stat analyses with the new habitat info.

Statistics, map, and the fair

My main project last week involved analyzing the data from the previous week’s cockle surveys and comparing them to the surveys conducted in February. Thus, much of last week was spent in the lab running stats and assembling maps on the computer. By now my GIS skills have sharpened somewhat, and I was able to assemble a map that compares the spatial distribution and densities of cockles in the July survey to those in the February survey. Although there does appear to be a difference, it seems random, and I cannot yet ascertain any significant conclusion from it. My mentor Scott was out of the office all week, so perhaps he will be able to provide some insights on Monday.

I’ve often told people that statistics is the math class I’ve been waiting my whole life for. I have yet to refine my abilities in it, but I find statistics a fascinating way to interpret data and answer questions of interest. The challenge in statistics for me is determining which method is most appropriate to use for a certain situation. Scott left me some suggestions, but it was still up to me to determine which method to use and how to interpret the results. I may have gone a little overboard: I ran two regression analyses of cockle weight vs shell length (one using the “raw” data, which turned out to be nonlinear, and one using transformed data to establish a linear relationship and constant variation); I also ran summary stats for both the February and July surveys. I ran ANOVA tests comparing cockle weights in July vs February and shell lengths in July vs February. I wasn’t sure if ANOVA was appropriate to use, so I additionally ran four nonparametric tests (two with one-sided hypotheses, and two with two-sided hypotheses) for cockle weights and shell lengths in July vs February. I generated boxplots, histograms, and scatterplots comparing cockle sizes and densities. On Monday I anticipate spending time whittling down the stats and analyzing the data. Scott will help me confirm my findings, but so far it looks like there is no significant difference in weights and shell lengths of cockles in July vs February. Maybe they just haven’t grown that much, or maybe I’m out in left field. Who knows?

Last Tuesday I helped staff the ODFW booth at the Coos County fair. We had a 1200-gallon aquarium with rainbow trout, baby cutthroat trout, baby smallmouth bass, and some perch. Despite the awesome showpiece, we weren’t very busy and didn’t have many visitors. It was probably due to it being a Tuesday morning, which constituted a slow day at the fair.

This week we’re scheduled to do a new cockle survey in a new location. We’re going to try and take down more data in the field this time, which should decrease the amount of time we need to spend in the lab. I also look forward to discussing the statistics with Scott and seeing if I’m on the right track with my data interpretation.

Sea Grant blog Earthdate 07/23/2012

Last week saw the beginning of my cockle survey project for Oregon Sea Grant. Those of you who are regular readers have probably surmised by now that this is one project among many. However, I anticipate this project to be more focused and self-directed than the others. That is, I expect to assume more responsibility for data input, processing, and analysis than for some of the other projects. This expectation has already proven true, but let me first briefly describe our field procedure: after generating 60 random points along with their latitudes and longitudes (sites for our quadrats) via GME software, I uploaded them to a GPS unit and generated a map in ArcGIS. Then on Wednesday Scott, Jim, and I journeyed into the South Slough of Coos Bay to gather specimens. With the aid of the map and GPS unit, we navigated to the various points on the mudflat near Indian Point and dropped our 1-meter square quadrat. For each of the 60 quadrats, we raked the mud within the boundary in two swipes: first we raked a straight line in one direction and recovered cockles; then we turned 90 degrees, raked a second swipe, and recovered any additional cockles. Specimens were taken back to the lab where I measured all shell lengths, weighed each cockle, and input all data into an MS Access database. Of course, I’m leaving out many details of the field protocol for brevity, but hopefully you get the picture. We repeated the procedure on Thursday but used a different set of random points. The most challenging part of last week was, as usual, working with the computer software to generate random points and the map. ArcGIS is a truly exasperating program when one has no prior experience in it. I’ve been successful in generating useful maps; it’s just taken way longer than I think/know it should (several hour sessions). I just have to keep telling myself “You’re a student. You’re here to learn. This is perfectly normal.” Robert Allan gave me some contact info during our meeting at mid-summer check-in for whom to talk to on campus about taking some intro classes in GIS—something I definitely plan to pursue.

Mid-summer check-in was cool. It was nice to see what everybody has been doing over the last month. It was nice to be in Corvallis and sleep in my own bed for a few nights. Although some of the kids got overzealous with the simulated cow poo (actually chocolate sprinkles) on the watershed model, the booth at DaVinci Days was fun to help staff, and I met a lot of cool people. The Little Feat show was a highlight. They put on an awesome performance, and I even got one of their guitar picks.

The week that lies ahead will see me processing data for the cockle survey: generating summary stats and histograms for comparison to the Feb survey, querying out database tables, generating ANOVA and maybe some non-parametric hypothesis tests, etc., etc., etc. The Red Rock crab study continues with surveys and tagging on Mon, Wed, and Fri. Tuesday I’m helping staff the ODFW booth for a few hours at the Coos County Fair. If you’ve gotten this far and are still reading, congrats! Lets see if I can include a few photos…

Rakin’ Clinocardium nuttallii

Close-up of 1 m quad with rake

Measuring a heart cockle

Crabs revisited, carpentry, and a BBQ.

Last week was pretty mellow and represented what one might call “more of the same,” but not in a bad way. In my last blog post I wrote that I was excited to begin my cockle project in earnest this past week. Well, turns out I got my dates mixed up, because that’s actually happening this coming week.

The week started off with some light carpentry work at a storage space in the marina. ODFW will be moving some supplies (boat, crab traps, waders, misc. tools) from one storage garage to another, and we needed to build some shelves to accommodate the gear. It was simple construction involving electric screwdrivers and circular saws and served as a reminder that jobs in fisheries science aren’t always spent in the lab or in the field. It’s important to have a variety of skills in any profession, I think, and be prepared to use them when circumstances demand. The rest of the day and much of Tuesday was spent in front of the computer practicing my GIS and database skills. Scott introduced me to a series of nautical charts from NOAA called S-57 charts. They’re fairly powerful in that dozens of geographic features can be added or eliminated to create a chart that’s suitable to one’s needs. I had to download an add-on for ArcGIS in order to use the charts, and after some initial frustrations was successful in getting it to work.

The rest of the week involved revisiting the Red Rock crab (Cancer productus) life history study. After some exploratory analyses, it was determined that we need more data, so on Wednesday Scott, Jim (another shellfish biologist at ODFW), and I re-deployed the crab traps in Charleston marina in an effort to capture more crabs for tagging. We set 13 traps throughout “A-dock” in the inner boat basin. Thursday and Friday mornings were spent measuring, weighing, and tagging crabs just as we had the previous week. By now I’ve gotten pretty efficient at it, and it’s something I’ve developed a real enjoyment for. I’m very interested to see how the data will pan out towards the end of the year.

On Wednesday one of the biologists brought his grill to work, and we had a cook-out for lunch. Burgers, hot dogs, salad, halibut—all the basic necessities were there. I have to say that I’ve been eating quite well here in Charleston. OIMB employs professional chefs who always produce wonderful feats of culinary creation. I don’t think we’ve had the same thing twice yet. Thumbs up to the meal plan.

This week’s agenda includes urchin sampling and the beginning of my cockle study (for real!). Cockle sampling will occur Wednesday through Friday, and since I will be in Corvallis on Friday for midsummer check-in, Scott says he’ll recruit an extra person to help gather data. Looking forward to more exciting experiences with ODFW. Will hopefully have more photos to share.

Another week of great variety in Charleston.

Last week once again saw me participating in a variety of activities for ODFW. On Monday and Tuesday, we finished the summer sampling session for bay crabs in Charleston marina. We measures, weighed, and tagged 325 (±) Red Rock crabs (Cancer productus) and 350 (±) Dungeness crabs (Cancer magister) in a week’s time (no tagging for these). The next sampling will occur in October, well after I’m back at OSU. I detailed the methodology of the study in my last couple of posts. Here I’ll briefly mention the purpose: Red Rock crabs are native to Oregon and, although they do not provide as much meat as Dungeness crabs, they are still sought after for the table. Red Rock crabs seem to be a sustainable resource—there are no size or sex regulations governing their taking—however little research has been conducted into their life histories. The study I’ve participated in, being conducted by Sylvia Yamada of OSU, is to assess various aspects of the life histories of Red Rock crabs in the Coos Bay area: how fast they grow, how old they get, how often they molt, and their movements between sites. We took measurements for the Dungeness crabs as part of an ongoing monitoring effort by my mentor, Scott.

Wednesday was, of course, Independence Day, and OIMB sponsored a nice BBQ for all the students and interns at Sunset Bay State Park. It was a good chance to get to know the staff of OIMB and talk to some of the students about their studies. However, the highlight of the BBQ was definitely culinary: grilled oysters on the half-shell. Yum!

Thursday and Friday were occupied by shore seining for salmonids in the morning and practice sessions with GIS, ‘R’ statistical software, and Microsoft Access in the afternoons. So far the computer activities have represented the greatest challenges for me during this internship. Up until now I’ve had zero experience with any of the afore mentioned programs, and I do not find them “user-friendly” in the slightest. Scott has been very helpful in writing some skeleton instructions and providing some basic activities to help me learn, but it’s still ultimately up to me to figure it all out. My learning has been through a combination of Scott’s guidance, online tutorials, and my own exploration/experimentation with the programs. This style of learning sometimes gets frustrating, because I tend to think in linear terms and prefer to have one source of info from which to work. I also admittedly find fieldwork much more attractive and exciting than sitting in the lab in front of a computer screen. However I have had some success in learning the programs, and I know it’s good to get outside of my comfort zone and experience a new style of learning. I also realize that skills in GIS and database management are essential to being competitive in the field of Fish & Wildlife science, so I’ve committed myself to spending a block of time each day to increase my proficiency.

For the upcoming week, I look forward to beginning my heart cockle study in earnest. So far, Scott and I have conducted a sort of exploratory study where we went out and investigated some sites in the south slough of Coos Bay and took some GPS coordinates. We also measured and weighed some cockles taken by a recreational harvester. These were basically introductory sessions to give me an overview of the fieldwork and protocols. This week, however, we’ll begin in-depth sampling of heart cockles and constructing the database. Stay tuned! More details to come!