What's in a thesis?

      2012 was the year of the thesis for me. For those of you that don't know me, I was a master's student at the University of Idaho in the College of Natural Resources.  I consider it a privilege and an honor to have had the opportunity to study there under the tutelage of an extremely knowledgeable, accomplished, and nationally recognized major professor.  In fact back in 2009 when I was trying to get in to grad-school pretty much anywhere that would take me, if you had asked me what my dream grad-school experience would be, I would have honestly told you that it would be to go to the U. of I., study under this particular professor, on a project dealing with salmon or steelhead.  So imagine my relief and excitement when the ONLY project that anybody offered me (and I was talking to people from literally all across the country) was there, with her, and studying adult steelhead!  Let's just say it literally could not have worked out any better for me, and I was, and still am, tickled pink.
     OK, caveats aside, let’s fast-forward back to 2012 again.  The fact that my dream master's project had kind of just fallen in my lap (after working my butt off to set myself up for it of course, but I digress...) doesn't mean that it didn't require a lot of blood sweat and tears (literally) to pull off.  Things were going great at the beginning of 2012.  I was a fair way into writing my thesis, which was the last thing I had to do in order to graduate; my classes were all done and my data was all collected, I just had to write and defend the thesis. If all went according to planned I was on track to having it done by about April or May; June at the very latest (and only if I would have done frivolous things like had a life on the weekends or only worked 10 hour days during the week).  The point is that things were going well and I was on track, until I was ever so gently reminded by persons who shall remain unnamed (you know who you are...) that the WHOLE point of me going to grad-school was to qualify for and get a good job.  This came about when early in February I started hearing rumors of a potential job opening which was right up my alley; in fact if there could have been a job description specifically tailored to my skill set and connections, this was it.  So not being one to look the gift-horse in the mouth, I applied for and was offered the job.  Great news, right? This means I'm finally a big kid with a real job and everything, right??  Right, BUT there was the "little" matter of the thesis. It was put very much on hold as I transitioned into the new job which was complete with three months of seven-day-a-week field work which started immediately. 
     I'm not going to bore you with more details than I have already bored you with, but let's just say that my thesis was delayed.... a lot.... I thought I would be finished in August until August came around, then I thought I would be finished in September until September came around... This wasn't for lack of trying mind you; I was working on it as much as I could muster without completely scrambling my brain.  I would work on it after I got home from work during the week, and all weekend long.  I had to try to walk the thin line between working hard and getting so burnt-out that my brain started to dribble out of my ears.  And what's worse is that even when I wasn't actually sitting at my computer typing, my thesis was ALWAYS on my mind, it was crushing, overwhelming, and scary.  There didn't seem to be an end in sight no matter how hard I tried to push through.  If I was a quitter, I probably would have thrown in the towel, but I'm not, so I didn't.
     In early September, my wife (who unfortunately was basically a widow and single parent for all of 2012) and I had a discussion and we decided that if I was ever going to finish, I was going to have to spend every weekend at my office at the U. of I. to work there until it was done.  I got more done there without all the distractions that come with working at home.  This strategy was not fun at all, but it worked.  The insurmountable mountain that was my thesis (which my wife and I had lovingly nicknamed "Voldemort" by this point) gradually became smaller and smaller until finally on December 7, 2012, I successfully defended it.  If you're not familiar with the thesis defense process, it consisted of a 45 minute presentation of my research in a meeting that was open to the public, then a private committee meeting with just me and the three professors on my committee who tested my knowledge and told me what needed to be fixed with my thesis.  By the end of that particular day, large portions of my brain were most definitely dribbling out of my ears.  I was given only minor edits from my committee, which was music to my ears.  Almost everybody has to make at least some edits, so the fact that they were only minor was awesome.  This was the biggest and most stressful hurdle that needed to be jumped before I could graduate.
     To celebrate my successful defense, I took my family to the Bavarian town of Leavenworth WA, for the weekend.  I think this was the best two day vacation I have ever had.  I didn't have to think about my thesis once that weekend and it was a complete joy to be irritated about how many people were crammed into the little town square, try to figure out how to pronounce “wassail”, or notice how weird red cabbage tastes.

Seriously though, there was a butt-load of people there.

Awesome weekend, and Leavenworth was actually a pretty cool little German town once the crowds dispersed a little.

     To make a long story short, I finished all of my edits on December 20th.  I had the whole thing printed on the required fancy paper then delivered to the College of Graduate Studies with literally two hours to spare before they closed down for Christmas break.  It was OVER and not a moment too soon!  Voldemort was dead!  To commemorate that special day I had a little ceremonial thesis burning - all 176 pages worth. 

Don't get me wrong, I'm proud of my thesis and very happy with how it turned out, but after 2012 "the-year-of-the-thesis", this was some much-needed therapy!

     So if you're still reading this you may be wondering "How do you talk about steelhead for 176 pages?" and that would be a fair question.  Let me give you the "elevator speech" version of my thesis, and maybe that will help:


     I studied the migration patterns and phisiology of post-spawning steelhead (known as "kelts").  Steelhead are anadromous, meaning they are born in freshwater streams, migrate to the ocean to grow big, then migrate back to the streams again to spawn.  Pacific salmon are also anadromous, and most people know that they die after they spawn (this is called semelparity), but unlike salmon, steelhead can migrate back out to the ocean, fatten back up again, then make another spawning run (this is called iteroparity).  This is an impressive feat because some steelhead migrate up to 900 miles from the ocean to their spawning stream and spend almost a year in the river before spawning, during which time they don't eat.  They sometimes bite and even swallow things - hence why we can catch them fishing - but their digestive tracts shut down while they're in the river so even when they do swallow something, they can't digest it properly.  They have to live on fat stores built up during their feeding in the ocean.  Any energy left after spawning can be used to migrate back to the ocean, but many don't have much left, and understandably so (you try swimming 900 miles upstream while not eating for 10 months and see how much energy you have left).
     In the Snake River basin in Idaho (which includes the Clearwater and Salmon rivers), less than 2% of steelhead are able to make more than one spawning run.  We don't really know if this proportion was always low since it's such a long swim to begin with, or if one of the many man-made changes to their environment including the 8 dams that they have to pass are making the proportion low. The goal of my study was to figure out how steelhead migrate down the river after they spawn, if the dams and reservoirs have an effect on their migration, and how their physiology relates to migration.  To do this I personally tagged over 300 kelts at six weirs in Clearwater River tributaries, and our crews tagged an additional 1,400+ kelts at Lower Granite Dam.

These are the eight dams on the Snake and Columbia rivers that the fish have to cross to get to Idaho, and cross again after spawning to get back down to the ocean.

If you don't know what a weir is, these are weirs. They are fish traps. The simplest explanation I've heard is that they're like a picket fence lined up across the river that leads the fish into a corral (the trap). Once they are in the trap, we could catch them, tag them, and study them.

Here is a map showing the locations of the three tributaries and six weirs (black lines) where we tagged fish. The yellow line is Lower Granite Dam.  Pay no attention to the red lines just yet, I'll get to those in a minute.

      Once we caught the fish we classified them as good, fair, or poor condition with the thinking that good condition kelts are probably more likely to survive and be able to migrate back to the ocean. Here are examples of each; you know, just in case you're curious.

Here's a good condition kelt.  Interestingly enough, this big humpbacked fella was caught just a few miles from the house I grew up in.  I didn't even know there were steelhead in there when I was a kid.

Here's a fair condition one. He's a little more beat up than the last one.

And last but not least, here's a poor condition one. The white splotches are patches of fungus - and no that's not a sign of good health - and yes I used a bunch of hand sanitizer after this picture...

      We tagged each fish to track its migrations.  We used PIT tags, which are about the size of a grain of rice and are injected with a needle.  These are the same kinds of "microchips" that you might have had put in your dog or cat.  Each tag has a unique code that is used to identify each fish while it migrates.  

A PIT tag with a dime for scale.  I'm planning on putting one of these in my earlobe someday, but I still haven't built up the nerve just yet.

      We also collected blood samples from the kelts. We used a centrifuge to separate the plasma which we then sent to Gritman Hospital in Moscow and a couple of other labs, to be analyzed just like a human blood sample for 20 different physiological metrics.  Some of the metrics are recognizable like cholesterol, triglycerides, and sodium, but others were more obscure and tongue-twistie like aspartate aminotransferase and lactate dehydrogenase. These different blood plasma metrics allowed us to understand things like how much energy each fish had left, how much tissue damage they had, and how well they were regulating the ions in their blood.

Extracting a blood sample from the tail of a kelt.  Cool blue gloves eh?

     I'll spare you the juicy details of all the analyses and statistics that I did on the blood data and just get to the point.  We found that kelts in good condition had better blood characteristics (higher energy level, lower tissue-damage, and better ability to regulate blood ions).  Good condition kelts also migrated farther.  This makes sense, you'd expect a fish that looks healthy to actually be healthy and be able to migrate better than a sickly looking one.  In fact according to the PIT tag data, fair and poor condition kelts didn't migrate very well at all.  All of the fish that were detected migrating in the lower Columbia River were in good condition; none were in fair or poor condition (suggesting that they simply died before getting that far).

Here's a graph of the cholesterol values from kelts in 2010. The different colors represent kelts in different conditions from each tributary.  You can see that good condition kelts generally had the highest cholesterol levels (In this case, high cholesterol is a good thing, it basically relates to how much energy they have left.).

     So knowing that good condition kelts were the most healthy and probably the most likely to make it back again, we decided to focus specifically on them and narrow down our objectives a little bit in 2011.  We wanted to see if they migrated differently in the free-flowing river and in the reservoir above Lower Granite Dam (the first dam they encounter as they migrate downstream).  To do this, we used a different kind of tag: acoustic tags, which were larger and had to be surgically implanted into the belly of each fish.  Yep, I'm a trained fish surgeon, I even stitched them up when I was done, cool eh?

An acoustic tag, about the size of the end of your pinkie finger, way to big for an earlobe...

Here's a kelt that I just operated on.  The little mark on the fish near my right pinkie is the incision site where the tag was inserted.

     In order to track the migrations of these kelts I deployed receivers all along the river to listen for the acoustic tag signals as the fish swam past (Remember the red lines from the map earlier?  They show where I put receivers).  Here's a video showing when and where we tagged each kelt in 2011, how fast they were going in each section of river, and how many of them made it down to Lower Granite Dam.  It'll be easiest to see if you watch the video in full screen mode (Mom, click on the little square just to the right of where it says "YouTube" right below the video).    

 We figured out several things about the fish by using these tags: they slow down when they get to the reservoir and they migrate faster than the speed of the water (meaning they are actively swimming downstream, not just "going with the flow".).  Also, all of the kelts we tagged made it at least down to the mouth of the Clearwater River (at Lewiston, ID), meaning that they made it through the part of their migration not affected by any dams or reservoirs.  A few started dying in the reservoir above Lower Granite Dam, and only 9% made it down to the lower Columbia River.  These are important findings because they imply that the dams and their reservoirs are negatively affecting the kelts.  If the reservoirs are slowing them down, that means it takes longer for them to get back down to the ocean where they can eat again (I don't know about you but that would make me grumpy if I hadn't eaten in 10 months...).  Also the fact that they have to actively swim through the reservoirs means they must use energy to do so, and at that point they don't have much energy left. 

In this graph you can see the speed (km per day) that the kelts were migrating at in different sections of the river.  The first two boxes on the left show the migration rate of two groups of kelts migrating from the weir to the Clearwater River mouth.  The uppermost portion of Lower Granite Dam reservoir starts at the Clearwater River mouth.  This is where they started to slow down.   The Little graph in the upper right corner shows when we tagged our kelts and  what the Clearwater River  water levels were like during that time.

        Finally, remember when I said that less than 2% of the steelhead in the Snake River spawn a second time?  Knowing this we didn't really expect many of the kelts that we tagged to come back, and not too many did - eight in all.  Previous research has found that repeat spawning decreased as migration distance increases, so we didn't expect any of our repeat spawning fish go too far inland, but they did.  We tracked three of the eight repeat spawners into the Salmon River, one of which was detected in the Yankee Fork Salmon River which is almost 900 miles from the ocean.  This was very surprising (and impressive!) and suggests that although it may not be common, repeat spawners can still be present in far inland populations.  Since we had blood data on these fish as well, we compared them to the rest of the fish and the ones that returned to spawn again generally had better blood metrics than the other kelts that we tagged. 


     And that in a nutshell is what my master's research and thesis was all about. If you're dying to hear more, feel free to give me a holler and I'll be happy to talk your ear off about it, heck I'll even send you your very own copy of my thesis so you can enjoy it for yourself!
     Overall grad school was a lot of fun and I learned more that I could have hoped.  I'm glad and proud that I'm finished, but at the same time I miss my friends and mentors there.  It was an awesome 2 years (plus a hellish third year...) and it was definitely worth it.
     This post is already long winded enough so I'll leave it at that, but I would like to share some of my other favorite pictures from grad school.  So here you go: 

I caught this eager little cutthroat on a tributary of the Lochsa River on one of my kelt tagging trips up there.  This is one of my favorite underwater pictures that I've taken.

Just a herd of butterflies....

I've got about 20 pictures of this tom turkey.  I noticed him while I was tagging kelts at one of the weirs, then when we finished with the fish I decided to try to call him in.  I didn't have an actual turkey call so I just had to use my voice (I can do a mean turkey call...).  Long story short, I called him in from a couple hundred yards away, got him to fly across a river, come within 15 yards, and stay there for 10 minutes!  He strutted back and forth, gobbled his head off, and tried his best to impress me! I wish it was that easy to do while actually hunting turkeys...

This is still my biggest sturgeon at 8 ft 2 inches (actual measurement, no guestimating here...). For the full story see this post.

I liked the pattern in this sandbar in Hell's Canyon.

I got to present my research at an international conference in Seattle, WA - pretty awesome!

A sunset over Puget Sound.

This is my favorite underwater picture of a kelt so far.

This cute little fellow is a juvenile lamprey captured at Lower Granite Dam.

Another kelt.  This picture made the front page of the annual report of our research unit at the U. of I.!

Sometimes dead fish have a rough life...  This is a Chinook salmon after her eggs were taken to grow more salmon at a hatchery, then we took a muscle sample and bone sample from her head to see how old she was.

This gnarly looking beast was 45 lbs of Clearwater River fall Chinook salmon! This was the biggest fish I saw while at the hatchery.

Scuba Steve!  I lost two acoustic receivers in the high flows in the spring of 2011.  They cost $2,000 each but I really just wanted the data that they contained.  Once the water came down in the summer I snorkeled to try to find them.  I found one, but one is still out there.  If you want to try, I'll tell you where to go and I'll give you 5... no $6 if you find it!

My family came to visit during some of my longer sampling trips.  Here we're checking out Selway Falls.

I had to figure out how to attach the acoustic receivers to various objects including bridges. Here our machine shop guy is putting the finishing touches on a fixture that they built (I designed it...) to attach a receiver to Arrow Bridge over the Clearwater River.

While "fishing" for kelts at the weir, we caught the occasional Chinook salmon. This was the first one of the year in 2011.

I saw some deers...

This old nasty hatchery rainbow trout got to be one of my practice fish during surgery training. He survived the surgery swimmingly, but believe it or not, he passed away shortly thereafter of a minor fungal infection....

One of my hobbies during downtime while camping and tagging kelts was collecting firewood.  I brought home what I could, then did this with the rest.

I discovered a hummingbird nest right next to my campsite, and in doing so discovered that hummingbird babies are stinkin' ugly!

This is Richard. He was my campsite buddy. He had a particular affinity for Cheerios.

Did I mention that Richard really liked him some Cheerios??

       Fwew! And that concludes the longest blog post ever.  Don't worry, I won't hold it against you if you didn't read the whole thing!