It’s hard to imagine what America’s prairies looked like when they were unspoiled. Today, more than 95% of our prairies and grasslands have been repurposed for agriculture. The last remnants are so highly fragmented that it’s a fight to keep non-native invasive species from taking over. Prairies and grasslands were once thought to be ecological wastelands, a monoculture of grass with not much productivity. From a distance, the prairie might seem like a boring place. But up close, prairies have the capacity to harbor more diversity than some forests. To really appreciate all that these grasslands have to offer, it’s best to visit in the spring when the sea of green gives way to shades of blue, purple, orange, yellow, and red. And it doesn’t just stop with color. Strange shapes adorn the prairie plants.
Prairie Smoke
Take the Prairie Smoke (Geum triflorum) for example. This plant has one of the strangest looking flowers you’ll ever see. It’s not an easy plant to find, but I managed to come across a fairly large portion of its habitat while out geocaching on Sunday.
I had discovered a cache called Broken Top a few months ago when the area was still too snowed out to visit. I figured that now might be a good time to go before the temperatures became unbearable. I also figured that this would be the peak bloom for most of the wildflowers. I was not disappointed. I picked up Wesley in Moscow and we headed down to Waha Lake for a day of exploration and geocaching.
For Memorial Day weekend, Waha Lake was decidedly uncrowded. It’s a small lake in the mountains south of Lewiston. There is a small municipal park at one end that serves as a campground. There’s nothing special about it, but the camping is free and it seems like a nice place to just get away for a night. The cache “Broken Top” sits near the summit of one of the “peaks” near the lake. You could probably access it directly from the lake via ATV trails, but we opted to drive up to the Idaho Fish&Wildlife parking area. The road up to the “trailhead” is amazing. As you ascend, you can look over the Lewiston-Clarkston valley and onto the palouse. This time of year, it transverses some open meadows that are full of wildflowers. It was during one of these that I noticed the Prairie Smoke. I stopped the car and we got out to look closer.
There’s no real trail to the geocache, so it was quite difficult to climb the hill without stepping on something that isn’t grass. There were so many plants in bloom that if I had stopped to identify all of them, we never would have made it to the cache. But, of the flowers I could identify, we saw Arrowleaf Balsamroot, Lupin (possibly two species), Prairie Smoke, Paintbrush (at least 2 species), Larkspur, Camas, Wild Hyacinth, Cat’s ear, some species of milk vetch. This list is in no way exhaustive, and perhaps I’ll return when I get back from vacation and create a more substantial list.
The scenic views from the geocache are nothing short of spectacular. In addition to looking over the Lewiston-Clarkston valley and the Palouse, you look straight down in to the Snake River. Across the canyon, the tips of the Wallowa Mountains peak up above the western rim.
Wesley and I set out to hike a bit and find some geocaches. We ended up with a magical adventure. Idaho never ceases to amaze me. I’d like to think that the place we experienced resembles the unspoiled Palouse, though I realize that the meadows we explored weren’t completely unspoiled themselves, nor were we actually on the Palouse. But it must have been a wonderful place before it was turned into wheat fields.
For all intents and purposes, 2013 was a shitty year. Just when we thought things couldn’t get any worse, something else would go wrong. And, so the trend continued until the final months.
The year started out pretty good. Though we’ve been struggling financially since Erin lost her nursing job in 2011, by the fall of 2012, she had a job and had enrolled at the University of Idaho to finally earn a bachelor’s degree to get her into a new career field. Â With snowshoes and a new (to me) pair of skis I acquired from the WSU swap in December, I vowed to stay fit during the winter so that by the time the hiking season returned, I could go farther into the backcountry than in previous years.
Deary and the Palouse from the summit of Spud Hill.
We had some early snowfalls last winter, so that by the time January rolled around, I was able to go snowshoeing with friends on a couple of trips. We started by taking advantage of the free day at the Idaho Park n’ Ski areas and headed up to Palouse Divide. Unfortunately, the trail we planned to hike had been cleared of snow as a logging road, but we had a good time. On the next trip, I headed up Spud Hill in Deary with CJ and ET. This is normally an easy hike, but with two feet of snow on the ground, it’s a good workout. We did make it to the summit for some awe inspiring winter views of the Palouse. The next week, we tackled the 5-mile Potlatch river trail. Our last winter hike would be to the Jerry Johnson hot springs near Lolo Pass. The snow on the trail turned out to be packed down, so we left our snowshoes in the car and enjoyed a nice walk through a winter wonderland with a relaxing soak in the hot pools. We finished January with a nice ski trip to Brundage with a large group of graduate students and post-docs.
February continued by following in January’s footsteps. The snowshoe trips waned as time commitments made it more difficult to get out. But then, during a weekend ski trip, everything changed. Until this time, I had never really broken a bone before. Then, on the last run of the day, I ended up in the hospital with a broken arm, femur, and tibia. That ended my physical activity for the rest of the season, and dashed my plans for a productive summer of hiking.
For the next few months, I concentrated on recovery. I still got out in the woods when I could, even for short trips or drives. By June, I was able to start bearing weight on my leg and start strengthening it in Physical Therapy. However, due to all of the inactivity, I had acquired a kidney stone, which was not fun to deal with. Fortunately, I passed it by the time I left for the Evolution Meeting in Utah, and I was able to complete some short hikes. In fact, I was able to climb to the summit of Mt. Baldy from the top of the tram at Snowbird. This was a major victory for me.
After the cabinets and some of the flooring had been removed.
Just as things seemed like they were getting better, we had a plumbing explosion at the end of July. Yes, we had not one, but three separate leaks. I was able to fix the one in the pump house myself, but the two in the kitchen required professional attention. In fact, that led us to getting a whole new kitchen and a string of headaches dealing with the contractors. And while we’re on the subject of our water system, we came home one day earlier in the spring to find that the water pump wasn’t working. It was a relatively minor problem that required a new electrical controller in the well, but it was still an expensive problem to deal with.
Finally, in September, Erin found out she was pregnant, only to find out a week later that she had lost it. While it was an early miscarriage, this was not her first, and she we had been actively trying to conceive for almost two years with no success. One more loss was icing on the cake.
So, it’s been a tough year for us emotionally, physically, and financially. But we’re pulling through. It hasn’t all been bad. I got my first peer-reviewed publication accepted, a project I had been working on since I started graduate school. I passed my preliminary exams and advanced to doctoral candidacy. And, I’m proud to announce a bit of good news as we head into the new year:
Yes, you are looking at that correctly. This is our child at 11 weeks. As of today, Erin is 13 weeks along and transitioning out of the first trimester. If all goes well, we shall be welcoming our first child into the world in early July.
Yes, 2013 has been a tough year, but it is ending with hope, promise, and optimism. This year shall be a valley as we climb forward through life. 2014 will bring challenges, but they will be good challenges, welcome challenges. I’ve been back on my snowshoes once this year and I’m looking forward to more adventures. My leg’s not quite ready to start skiing again, but I may give cross-country skiing a try, since there are so many great opportunities around here.
I stand here looking forward without looking back. Good riddance to the old year, and Happy New Year.
It’s been over a week since a Northern Hawk Owl was spotted hanging out across a busy street from a shopping mall in Moscow, Idaho, but the bird is still here and reliably seen in the same locations. I’ve now seen the bird four times and may continue to watch and observe it until it is no longer a novelty. Of course, that might be all winter, and the owl might actually leave town before seeing it is no longer exciting.
Today’s viewing was special. The sun came out and temperatures finally rose above freezing, making it bearable to actually spend more than fifteen minutes chasing the bird. Simon, a friend and coworker of mine, came out with me and brought some telephoto lenses to help us get some better photos of the owl. Unlike the images in the last post, these are not cropped.
The latest rage in Moscow, Idaho is the sighting of an immigrant that shouldn’t be here. A Northern Hawk Owl (Surnia ulula) has been spotted in Moscow across Rt. 8 from the Safeway parking lot. The earliest sightings on eBird show that this individual has been hanging around since Tuesday, reliably in the same spot.
This is an exciting discovery because the Northern Hawk Owl isn’t supposed to be seen this far south. It’s native range is exclusive to Canada, and visits to the United States are few and infrequent. It’s unclear at this time how long the owl will stay in Moscow. It’s likely to be a short-term visit, though some Hawk Owl sightings in other locations have lasted an entire winter. With any luck, it’ll hang around long enough for me to get some more photos, and maybe even procure a nice telephoto lens to shoot it with. I expect that this sighting will bring in birders from across the northwest, and even beyond, who wish to add such a rare and magnificent species to their life list. For birders and wildlife enthusiasts who live in Moscow, we are incredibly fortunate, for an opportunity such as this may only come around once in a lifetime.
The Northern Hawk Owl belongs to a minority group of owls that are diurnal, hunting during the day rather than at night.
Since we finished the interior of the house, it was time to clean up the garage and start moving everything back inside. This was also a good time to start tidying up the yard before winter hits. Last weekend, we took down an old dog house that we were using to raise chicks in since the chicks are now old enough to roost in the main hen house. When we picked up the structure, we found that the chickens weren’t the only ones using it for a home.
And now for some other cuteness:
Mower and Jasper were cuddled on a piece of plywood.
Three months ago, we had some pipes leak in our kitchen that caused some damage to the flooring and the cabinets and resulted in us basically getting a brand new kitchen. We contacted State Farm to see about getting any coverage, and thankfully, they agreed to help cover some of the damage. So, we set about getting a contractor in to look at the damage and give us an estimate. We ended up using one that works directly with State Farm, a decision that may have caused us more strife that we were hoping to avoid, but after several delays, screw-ups, and mis-communication among the different workers, we finally have our new kitchen (and living room).
The photo above shows what the kitchen used to look like, though the island had already been removed. It wasn’t a bad kitchen. In fact, it was originally one of the reasons we liked this house. There were a few things we had wanted to change eventually. The pantry on the left blocked one of the electric outlets and took away some valuable counter space. Mostly, though, we were getting sick of the color scheme. The green and yellow can be bright and cheery, but it was also getting dirty. It was left over from the previous owner, and we wanted something that was ours. Since the kitchen had to be torn apart, we took this time to re-paint both the kitchen and living room, which is really just one big room.
After the cabinets and some of the flooring had been removed.
When the contractors first came out, we were under the impression that they would be able to get everything out and replaced before school started. However, we waited about 3 weeks before they even came out and started removing the cabinets and wet flooring. In this time, the smell of mold became more and more intense to the point where we had to call them to come out and remove the damaged pieces. They set up a containment tent with their portable air filtration unit to dry out the place and get rid of the mold. That lasted for several days, during which we were slowly moving furniture out of the living room since the entire floor would eventually have to be replaced. We had a plumber come in and replace all of the steel pipe with plastic tubing. After that, we found that we could drink the tap water right from the sink without any extra filtration. Turns out it was the pipes in the house that were causing us to have rusty water. No wonder the pipes burst.
The contractors finally came and removed the rest of the floor, but neglected to order the new flooring that we wanted. Instead, they kept bringing us samples that were darker than we desired. Finally, we went to Home Depot, chose the flooring and gave them no choice but to order it. The Vermont Maple Pergo® XP looks great, by the way.
The flooring wasn’t the only hang-up. We wanted to order some nice assemble-yourself cabinets that were cheaper than the custom cabinetry at any of the building supply stores have, but better than the pre-assembled cabinets in stock. They came in to measure the walls and gave us a layout using the in-stock cabinets. Apparently, they measured incorrectly the first time and we had to wait longer for the designs to come in. At that point, we begrudgingly went with the cheap in-stock cabinets. They were to paint them white. When they came and installed them, they were barely painted. We could see the wood grain through the paint, which was unacceptable. We were ready to get rid of these guys and call a new contractor to finish the job when they came and re-painted everything.
So, what we thought would be a two to three week job ended up taking three months. Last week, they came in and made all the final touches which left us with the task of finishing up any last bit of painting, which we did this weekend. We have one wall in the back bedroom to finish painting, but as that room is mostly storage at the moment, it’s not on the immediate priority list. We still have some little work to do such as painting the island white and installing handles on the cabinets. We now have more counter space, more cabinet space, a bigger and deeper sink with a working spray hose, a dishwasher, a fan over the stove, and a nice bright new color scheme. I present to you the new kitchen.
After everything is done, we have more counter space, more cabinet space, a fan over the stove, and a dishwasher.We still have to paint the island and add handles to the cabinets, but the kitchen is otherwise complete.The living room with its new color scheme.
Where has time gone? It’s already October, which means I missed out on September.
Well, I didn’t really miss it. I was busy with a graduate school ritual known as the preliminary examination. Prelims are, without a doubt, the most stressful event for a graduate student. You might think it’s writing the dissertation or even giving your final defense. The truth is, by that time, you know your subject inside and out. Writing takes time, and the stress is making the deadlines, but overall, unless you slept through your graduate student experience, writing up the dissertation isn’t that difficult. The defense, generally structured as a 45-60 minute seminar followed by a couple hours of grilling by the committee, isn’t as stressful because, as I mentioned before, you know your subject inside and out, sometimes better than your own major professor and committee members.
Prelims are another story. The purpose of prelims isn’t really to test what you know, but to test what you don’t know. If you don’t know the basics in your field, then you’re not ready to be a doctorate. The structure of prelims varies from school to school, and even between departments within a school. For example, the BCB (Bioinformatics and Computational Biology) students at the University of Idaho have to write a research proposal, present it as a 45-minute seminar, and then defend it in front of their committee members. This is their prelim. The biology department is a bit more traditional. The proposal process is separate and prior to the exam and is all behind closed doors with the committee. The prelims consist of a written exam in 3 subject areas and an oral exam two weeks later. It’s up to each student/committee whether the written exams are closed or open book, whether they are timed or take-home essays, and so forth. My exams were four hours each, split over three days. Barrie gave me 7-8 questions centered around animal behavior, quantitative genetics, and evolutionary biology, and I was to answer four. I felt that this format took some of the pressure off of me, though you never really know what your committee members expect out of you.
If you’ve taken prelims seriously and studied hard prior to the exams, then the testing itself turns out to be not so stressful. The major source of stress is the anticipation, and the uncertainty of knowing just what is going to be asked of you. As a result of this tension, I over-prepared for much of it, but in the end, that worked out in my favor. One of my committee members is known for being a hard-ass. Or so I thought. It turns out, he really wants students to understand the basics. When you don’t meet that expectation, it seems as though he’s being hard. It turns out his questions were very fair. In fact, a few seemed very simple compared to my expectations. Even in the oral exam, he wasn’t the toughest in the room.
Over-all, my committee was pleased with my written answers, and I think that reflected in the orals. Typically, the oral exam is where your committee really throws curveball questions, looking to see how you respond when asked to answer questions they don’t expect you to be able to answer. And, so I knew this and was prepared to admit lack of knowledge when it was there, while making sure I could answer the relevant questions to my field of study. The oral exam didn’t even last two hours. When I was asked to step out while they deliberated, I was pretty sure I would pass. I wasn’t expecting to come back in hearing some suggestions for research ideas.
So, on September 19, almost two weeks ago, I officially became a Ph.D. candidate. And with some relief from the stress of prelims, I now embark on the stress of writing an NSF DDIG grant proposal, of which I have a week left to finish, assuming the government re-opens and the deadline hasn’t changed.
The tomato plants have fruit, but I’m awaiting them to ripen. The pepper plants are starting to produce. The strawberries are on their second round of harvest. In the mean time, the squash and zucchini are providing us with food of plenty. Yesterday I picked four zucchini, all from the same plant. This morning, I grabbed two more before leaving for work. This doesn’t include the half-dozen or so that we’ve already picked and are awaiting consumption in the kitchen. We’ve also got several variety of yellow summer squash as well as two green stripped squash/zucchini plants, both producing about a fruit a week.
It’s getting to be overwhelming. How are we going to keep up with all of this produce? Aside from Erin’s love of zucchini, we’re not eating it nearly as fast as we did last year. It looks like I’ll be breaking out the dehydrator again to make some zucchini chips, great for just snaking on while lounging around the house. Erin also made some zucchini break last night. She made one gluten-free and egg-free loaf that tastes good, but didn’t really cook through properly. But such is the plight of making gluten-free pastries without eggs. The regular loaves turned out great. I had a piece fresh out of the oven last night a la mode for dessert, and two more pieces for breakfast. With all this zucchini, bread might become a staple over the next few weeks.
Exhibit 2. Kabocha Squash. Specifically red kabocha squash. These look like pumpkins and are sometimes referred to as pumpkins. These winter squash originate from east asia and are supposed to be very pumpkin-like in usage. They’re sweet and can be cooked down and used in pies, soups, pastas, and stir fries. In fact, when looking up these squash, one of the first things I found was a recipe for kabocha squash with thai curry. With so many options, I’m not sure how I’m going to use the few that I have. But these squash seem to grow better than the pie pumpkins around here, so I think we’ll look to put more in next year.
We tried growing watermelon this year. Erin bought a variety that doesn’t grow very large, though I was expecting fruit a bit larger than what we produced. But we actually did get some watermelons and tried the first one Monday night. It was either not ripe enough, or too ripe. I’m not sure. Much of the flesh hadn’t turned pink yet (or maybe the rind grew too thick?) and it just didn’t taste sweet. I maintain that we took it off the vine too early, though Erin thought they were ripe. We have a second one that we’ll wait to cut into, hoping that it will ripen more off the vine. Overall, the watermelons didn’t do so well. One pile of plants barely grew, the other grew sufficiently, but the leaves were always curled, a sign of not getting enough water. I think that the location of our property is just too dry to support a crop that needs a lot of water. Maybe I’ll try again next year, but it won’t be a main focus of the garden.
Overall, we seem to do well growing squash and leafy greens such as lettuce, spinach, and chard. The greens are particularly happy early and late in the season when temperatures are cooler. I’ve already removed several rows of lettuce that have bolted, but replaced them with new seeds that are already sprouting. We should have lettuce well into the fall when everything else has succumbed to the frost. The sugar snap peas grew well once we were able to keep them from getting eaten. Next year I’ll try using peas and beans to shade the lettuce. Tomatoes and peppers always struggle to ripen as the growing season comes to a close. But I love growing them, and one of these days I’ll figure out how to get them to harvest early on. It’s funny that we’re only 25 miles away from Moscow and not much higher, but the growing season is significantly shorter.
When we moved to Moscow, we knew we’d be here for more than five years and that buying our own place would probably benefit us more in the long run than renting. There are many advantages to owning your own home. The most obvious is that your monthly payments go toward something tangible. When you pay rent on an appartment, all you get back is a place to live for the month. With a mortgage payment, you’re that much closer to actually owning the place you live in, which means when you move out, you can get that money back by selling the place. It’s also freeing. We can do whatever we want to the house without having to ask permission. Don’t like the walls? We can paint them. How about a new floor? Done. Want some pets? Nobody to raise our rent for having them, or outright deny us the choice to have them. We have our own yard that we can decorate and landscape as we please, including putting in a vegetable garden.
Of course, owning a home isn’t all freedom and bliss. It costs money. We still have to pay utility costs, but when something breaks, we’re also responsible. There’s no landlord to call to have it fixed. Such is the case when we found not one, but two water pipe leaks this past week. The first leak was in the pump room in the garage. The pipe leaving the presure tank was connected to the pressure T joint via a steel coupling and a nipple. The nipple, threaded into the T, had corroded its threads and developed a small spray that was slowly getting bigger. So, when Tate came over to help me take off the broken pieces, he thought the threads inside the T had been stripped away. It was later that I found the threads to be just fine, only dirty with build-up and possibly the threads from the pipe that had come out of it. The pressure T happens to also be threaded on the outside, so I bought the proper step-down joint and repaired it. When I got the water back on, the leak had been repaired.
But it was still dripping water. This time, it was coming from the base of the quarter-inch pipe where the pressure switch connects to the T. We had some plumber’s putty and used it to try and temporarily patch the leak. It worked, sort of. The leak persisted, but had slowed to a very slow drip by morning. However, the putty should seal a small leak like that. It turns out the putty we had bought was old and starting to dry out, causing its application to be quite difficult. We picked up a fresh pack and attempted to seal the leak again. In doing so, the leak got worse. When investigating the problem, I noticed that the pressure switch wobbled quite a bit and I thought that maybe I could screw it down tighter. So, I disconnected it and soon discovered that the pipe was indeed corroded and the threads had snapped off.
In the end, I got a new pressure T and replaced the steel pipe with PVC, as the rest of the pipe had already been converted. The old iron pipe had been connected to the new PVC with a self-adhering coupling. I figured I’d use the same method which would give me an easy disconnect point should I have to take the pressure T off again in the future. Of course, on first connection, I must not have had the coupling lined up quite right. It was very difficult to screw into place and after turning on the water and noticing a small leak, the coupling slid right off the new pvc making a mess of my pump room. After some fiddling around, I got it to fit properly, and so far, there have been no leaks in the pump room.
The second leak was in the house. Erin came home from her work trip to Dinosaur National Monument and noticed that the floor in the kitchen had buckled a little bit, indicating it was wet. She then heard a small leak which we thought was coming from under the floor. But our floor is solid concrete under the laminate. As we started to tear it up, we noticed that the leak was coming from pipes behind our kitchen counters. So, while Tate was out, he helped me remove one of the cabinets which, thankfully, wasn’t installed correctly and was quite easy to remove. Again, the leak was between a steel nipple and a T-joint. The nipple had corroded through its threads spraying water against the cabinets and leaking down into the particleboard subflooring. We were able to remove a small section and replace it with pex tubing and sharkbite connections. The leak has been patched and we now have working water again. It was good to take a shower this afternoon.
The aftermath of this leak is going to be the more difficult part. Because the cabinets and subflooring are made of particle board, they quickly absorb water. We’re not entirely sure how long the pipe has been leaking, but there was a mild odor of mold and mildew. Even if the cabinets aren’t pemanently damaged, the subflooring and the floor pannels are. We’ll still have to rip out the cabinets to repair the flooring underneath and assess any other damage to the wall. In addition, these failures have us worried that more junctions are going to fail in the near future, so we’re contemplating having all of the steel pipe replaced with pex or pvc while we have the cabinets out. Worst case scenario, we’ll have ourselves a completely remodeled kitchen. At least if the damage is bad enough, our insurance policy will help cover the repair.
The joy of home improvement projects, voluntary or involuntary, is that you come to realize how many tools you need to be a home owner. It’s not enough to have a hammer and some screw drivers. Thankfully, Tate had some pipe wrenches for us to borrow for now, but I think I’ll be investing in at least one in the near future. There are some jobs that you just need a professional for. Fixing the kitchen may be one of these. But by repairing these small plumbing faults ourselves, we likely saved a couple hundred dollars. I’m not happy about the circumstances, but it’s nice to know that some problems aren’t as difficult to fix as you might think.
Last week, the fruits of my last three year’s work has finally come to fruition in the journal PLoS One. The premise is that the personality behavior we call boldness, or the bold-shy continuum, is not only heritable, but a genetically correlated multivariate trait. The research is essentially a continuation of a project Mary Oswald completed for her dissertation, however upon first submission, reviewers criticized the study for its lack of replication. So, in the Summer of 2010, she set up a second selection experiment which I took over and have been maintaining since.
Boldness is an interesting behavior to study in animals. As a personality behavior, individuals with a particular boldness score relative to the population tend to remain that way for the long-term, and while there is some plasticity between contexts, individuals that are bold tend to remain bold, and individuals that remain shy tend to remain shy, and populations can evolve toward one end or the other based on selection pressures. Of course, the best way to really get this point across is to see some videos exhibiting just what boldness and shyness represent.
These are Zebrafish, Danio rerio. The top tank, labelled “Nadia,” contain a wild strain, but these fish aren’t taken directly from the wild. Instead, these are the 4th generation from wild fish to be raised in captivity right here at the University of Idaho. Notice how they prefer to swim at the bottom of the water column and shy away from a human presence. Now contrast that with the bottom tank containing fish from the Scientific Hatcheries (SH) strain, which are more than 30 generations removed from captivity. They not only spend more of their time near the top of the water column, but are also un-phased by a human presence. In fact, if they do react, it’s to come closer to a human observer rather than to shy away. This observation in contrasting behavior between wild and domestic populations has been repeatedly observed in a number of different species including trout, salmon, birds, mice, rats, dogs, and foxes. The question is: why?
Now, your first thought is that this might be a result of rearing environment. Domesticated animals grow up around people and are therefore not afraid of them. But, remember that both of these populations were reared in the same environment. The “wild” fish have never seen their native habitat and were raised with the same human contact as the domesticated fish. When the environments are equalized, differences must be due to genetic differences.
One way to test this hypothesis is to select upon these behaviors. Simply put, selection doesn’t act on a trait if there is no genetic variation controlling variation in that trait. We took a random sample of 80 SH individuals and behavior-typed them by taking 24 point observations over the course of a week scoring whether they were within one body length of the front of the tank near the observer, or not. The observations are averaged to create a “boldness” score. The five highest scoring males and females were mated to create a “bold” line, and the five lowest scoring males and females were mated to create a “shy” line. For each of these observations, we also recorded the location in six vertical depth zones to come up with a depth preference measure. Once each day, we measured feeding latency, the time it takes for an individual to feed from the surface of the water.
After two generations of selection, we were able to estimate the heritability, that is, the proportion of behavioral variation that is attributed to genetic variation, and the genetic correlations using a REML analysis. The gist is that these three behaviors have a significant, but moderately low heritability (between .25 and .3) and fairly strong genetic correlations (between .6 and .8). What this means is that selection can, in fact, act on these behaviors, and that selecting on a single behavior will also induce a response in the other two. As I stated earlier, these results have finally been published in PLoS One, and because it is an open access journal, you can actually read the paper free of charge.
One of the implications here is that the behavioral differences between captive and wild populations of the same species are due to an evolutionary response to the captive environment. Of course, it could be that in captivity, humans will artificially select for bolder behaviors either intentionally, in the case of the pet industry, or unintentionally, either by selecting on traits that are correlated with boldness, or because bold individuals are simply easier to catch for the mating process. However, there is a hypothesis that shyness is selected for in the wild by predators (we assume that a human observer represents a potential predator), and that in the absence of predators, boldness might be the more fit phenotype. Bold individuals are risk-takers. They’re more likely to be seen in the open foraging for food where they are in risk of getting picked off by a predator. Shy individuals are more likely to hide and wait until it is safe to eat. The trade-off is that while bold individuals risk their lives, they consume more resources which they can invest in growth and reproduction. On the other hand, shy individuals live longer, and might produce more offspring over their lifetime. In the absence of predation, bold individuals will still frequent the open habitat and feed sooner than the shy individuals, but they won’t be picked off. Thus, there is the potential that they can produce a higher quantity and quality of offspring than shy individuals in captivity. This is also confounded by the observation that shyness is correlated with anxiety and stress. Highly stressed individuals are unable to allocate as much energy toward reproduction compared with unstressed individuals. Anxious animals in captivity don’t breed as well, and we’ve noticed this trend while trying to breed our wild lines of zebrafish in the laboratory. I hope to test this hypothesis in the near future by bringing in some new populations of zebrafish from the wild and measuring fecundity and behavior.
In addition to linking boldness with fitness, I’m also interested in the nature of the genetic correlations among our three boldness components. Heritabilities and genetic correlations are population specific. Just because we’ve estimated these numbers in one population does not mean they hold true in another population. That is because heritability is linked to allele frequencies, and those are going to change from population to population. In fact, they’re going to change within a single population over time, especially if selection is acting upon the traits. Genetic correlations, on the other hand, can be somewhat stable depending on their origin.
There are two ways to generate a genetic correlation. One is to create linkage disequilibrium (association of alleles at one gene with alleles at another) by selecting on two or more traits simultaneously. For example, if blonde hair and blue eyes were preferred traits in a population of humans, the genes for each trait would fall into linkage disequilibrium. Normally, recombination would disassociate the two traits from one another, but with preference for both, blue eyes and blonde hair would both rise in frequency in the population in such a way that if you sample an individual at random, he’d likely have both blonde hair and blue eyes. Since the traits are now correlated, selecting on only blonde hair will still select for blue eyes because the occurrence of blonde hair and brown eyes is relatively low.
The other way to generate a genetic correlation is if two traits share the same genes, also called pleiotropy. Suppose eye color and hair color are controlled by the same gene. In this case, the allele for blue eyes (lack of pigment) also produces blonde hair (lack of pigment). If these traits were controlled by a single gene, it would be impossible to disentangle hair color from eye color. However, quantitative traits such as these are much more complex. There are many genes that control your hair color, and many that control your eye color, and it’s likely that some of them are shared through pleiotropy, but many of them are not.
In this respect, I am interested in understanding the genetic architecture of boldness. How many genes likely control each behavior and are they linked through pleiotropy? How similar are the correlations in other populations? There are a number of ways to get at these questions. One is to perform a QTL which involves looking at variation across the genome for areas in which genetic variation correlates with behavioral variation. In doing this, we can begin to understand how the genome can influence behavioral traits. The other is to measure heritability and genetic correlations in other populations. The resulting G matrixes can be compared, mostly looking for rotation. If the matrixes align, then correlation structure is conserved. That isn’t conclusive proof that each behavior is linked by pleiotropy, but it might explain why the same sorts of behaviors vary in the same direction between wild and domestic populations.
In other words, behaviors associated with the bold-shy continuum may be constrained to always evolve together during domestication events. That is the overall hypothesis and theme of my doctoral dissertation.
Because I was laid up and out of commission for much of the spring, I wasn’t able to work on expanding our garden much this year. Last year, I built a third 4×8 foot box and a 2×4 foot box which were meant to be tiered for planting small annual herbs in large quantities. I never got that box filled with dirt, so that will have to wait until next year.
In the mean time, we’ve planted our usual array of crops in the two 4×8 foot boxes with limited success. Erin had bought some tomato plants in April, and although I warned her to wait, she planted them anyway. We had one last frost in early May which killed the plants, so we had to start over again. We bought a lot of plants toward the end of may: 3 tomatoes, 4 peppers, a whole bunch of squash, and a few more strawberries. We also planted spinach, lettuce, basil, cilantro, parsley, peas, and chard seeds directly into the beds. A few days later, we noticed that the chickens had somehow gotten into the garden, eating most of the seeds and stirring up our nice rows. It took us a few weeks before we had the time to go back and plant again. In the mean time, a few seeds remained and sprouted. I carefully dug up the remaining plants and re-arranged them into rows while we put the rest of the store-bought plants into the beds. After a week of constant rain, most of those seeds have started sprouting, so we’re bound to have some crop this year.
Meanwhile, the strawberries are happy as ever. We’re getting a bowl-full each day, somewhere between half and one pound. Though the berries are smaller than the ones you find in the stores, they pack much more flavor. Of course, it wasn’t always this way. When the strawberries first ripened, I would pick a few here and there, but find most of them had already been eaten. I had noticed a robin hanging out by the strawberry bed, so while I was away at Evolution, Erin bought some mesh netting to throw over the plants. Since doing that, we haven’t had a problem with the birds. I think we might try to double our strawberry patch for next year in order to produce enough to make jam. We’ve also started some raspberry vines, which aren’t looking so great this year  because they sat in a bucket too long, but they’re starting to put out new shoots and leaves, so next year we should have a small harvest.
We have some tomatoes, peas, spinach, chard, and letuce growing in this box.There’s a tomato, spinach, peppers, lettuce, basil, and cilantro.
This year, we planted a variety of squash and watermelon.
One of my projects this year is to eliminate the grass between the boxes, putting in nice walkways instead. I’ll use a combination of cardboard, newspaper, and straw to mulch over the grass and eventually cover with wood chips. This should help keep weeds down, eliminate the need to whack back the grass, and create aesthetically pleasing walkways. By the time we leave this place, we should have built up a nice productive garden for the next occupants to use. Maybe I can even get a greenhouse.
Given my current disabled condition, there’s not much I can do to get ouside and enjoy the sunshine, but there are a few places that I can go. There are paved walking and bike trails in every nearby town, and some of them offer spectacular scenery. The Trail of the Coeur D’Alenes, for example, starts in Plummer and meanders for over 70 miles to the town of Mullan near Lookout Pass. There are some sections of this trail that seem like they’d be good to explore, but this time of year, there might still be some snow blocking my way or even some downed trees across the path.
Fortunately, Lewiston’s Levee Parkway doesn’t suffer from either of these problems, and it has the added benefit of an extra 5-10 degree increase in temperature. The levee lines the Clearwater and Snake Rivers and was built for both recreation and flood control. The 11-mile trail begins near the Rt. 12 bridge and ends at Hell’s Gate State Park. There are views of the river, the canyon walls, and some of the more industrial sights of town, but overall, it’s not a bad spot to be, especially in my condition. In fact, I kinda wished I had my camera on me even though I’m not sure I’d be able to support it with two hands yet.
It does have one other attraction. The spill-over ponds on the other side attract migrating waterfowl, and people from all over the state will come to Lewiston to witness this display. Yesterday, I must have counted about 15 different species of water birds, and there were probably more that I missed because I lack a spotting scope. It’s not just the number of species that is awe inspiring, but also the sheer number of birds. Between the ponds and the river, there were probably thousands of bodies floating on the water.
My complete list of sightings for the afternoon can be seen here. In the upcoming weeks, I’ll be checking out other trails for the disabled, many of which travel through great bird habitat. While I may not be exploring the backcountry as I once was, at least I can still get out and have some fun. And pretty soon, I should be able to hold a camera again.
February 17th began as any other trip to McCall. I rolled out of bed around 5:00 am, packed the car with my gear, and 20 minutes later, I was leaving for Moscow to meet up with Tyler and Genevieve. We made it to Brundage around 10:30 local time and headed straight to the Centenial chair where we met up with Chloe, Ben, and some of Chloe’s family. We had a good day on the mountain, but stuck to the groomed runs and trails because there hadn’t been any fresh powder in over a week.The first thing we noticed was how crowded the resort was. This was the first time we had to wait in line to ride Centenial. Later on, we headed over to Bluebird Express where the wait for the lift was ridiculous. We skied a short day, but really, we got in more runs in four hours than we would normally get playing in the trees on a full day. We came off the mountain exhausted, but happy that we had chosen to come down this weekend.
After winding down with a few drinks in the lodge, we headed to the hotel to check in and change for Tyler and Gen’s maternity shoot. They had offered to buy me two days of skiing in exchange for a couple of photography sessions, and we decided to cash in on one of them at Ponderosa State Park. It was fun, and some of the results are available here. We closed out the evening with a soak in the hot tub at the hotel and called it an early night so that we could get an early start on Monday and beat the crowds.
The funny thing is, for a 3-day holiday weekend, we barely saw any people on Monday. This isn’t the first time I’ve noticed this trend. On Memorial Day and Labor Day weekend, people seem to clear out Monday morning leaving trails and campgrounds wide open. Their loss, I guess. It was nice to have no lift line and and no crowds of people to dodge on the slopes. I decided to bring the GPS with me to track stats for the day.
Tyler and I took our first run down the speedy 45th Parallel, one of my favorite runs of the mountain. 45th starts with a nice drop to get you going but continues on a fairly straight track. It “levels” out a little about 2/3 of the way down, and then drops down along the ridge spine around a small curve to the steepest part of the drop. You can build up quite a bit of speed here if there aren’t too many people in front of you, and generally it’s ok to do so because the drop ends with a long level runway leading to the lift. I tend to head into a racing tuck to take the last drop and then stand up and let my coat parachute me to a stop. On this run, I made a top speed of 68.8 mph, and that would remain my top speed for the rest of the day.
The other great run for building speed is Alpine. This is also the run used for races. Alpine starts between the Bluebird and Centenial chairs and pretty much descends straight down the face of the mountain. It’s not as steep as 45th Parallel, but it can still be fun. In fact, the allure is a short up-hill cat track to the top of the Bear Chair lift, and the goal is to make enough speed to get to the little snack hut atop the knob without any pushes or skates. This is where I clocked myself at 58 mph last year.
Overall, it was a fairly quick day. In an hour, we had completed four full runs down the mountain, each run about 1.5 miles and 1600 feet of vertical drop. When we met up with Chloe and Ben, we put two more runs behind us. The longest run was a 2.5 mile 1800 ft. decent from the top of Bluebird to the bottom of Centenial via Lakeview Ridge and Temptation. It takes about 10 minutes due to some cat track sections, but it’s a fun one to take. On the 12th run, I challenged Ben to a mogul run, which he took with no sweat, but I took much slower.
And then there was the last run of the day. Apparently, there is much dread around “the last run” that many people just don’t even take it. Hell, even my last ski accident in 12th grade was on a “last run.” On this run, we chose to finish on Engen, a trail that follows the Centenial lift most of the way down the mountain, but affords us an easy access to the lower parking lot where the car was located. In hindsight, there are a number of decisions I made that, if done differently, could have altered the outcome of the day. My friends all turned off of Engen onto Skid Row. I decided to keep going and ride the cat track at the bottom out to the car. I was running the trail quite well and thought that maybe I could beat my speed for the day. But really, I should not have taken the last run of the day so fast. It’s one thing on fresh legs. It’s another when you’re tired and ready to quit. I should have had my edges sharpenend as I was having trouble making sharp turns. But most of all, I just shouldn’t have chosen this trail for a speed trial because it does turn into a cat track rather than make a straight run. As I descended that final drop, I knew I wasn’t going to make it onto the cat track. And so, in the final seconds, I decided to hit the snow and slow down as much as I could before smacking into the trees. I was thrown into the air and landed uncomfortably on my side. I couldn’t move. I knew something was broken. I immediately started calling for help.
It wasn’t long before another skier came by and stopped to help. He got my phone out of my jacket and called for the ski patrol. I wasn’t aware of it at the time, but someone on the lift saw the whole thing and also called 9-1-1. It seemed like an eternity before the ski patrol finally arrived, and even longer before they were able to transition my mangled body onto a stretcher. By that time, I was getting sore from laying uncofortably and cold from lying on the snow. I would only begin to feel the pains of my injuries after being moved and stabilized. They skied me out to the lower parking lot, hooked me up to a snowmobile, and brought me to the upper parking lot where an ambulance was waiting to take me to the McCall hospital.
Once I was warmed up and pumped full of pain meds, I felt fine, at least as fine as I could be in that situation. Luckily, I had no head injuries. I attribute that to my quick thinking moments before hitting the tree. But it could have been bad. I wasn’t wearing a helmet, and the GPS recorded me at 51 mph when the impact occured. So what are the final results? I broke my left humorous into 3 pieces, severed my right femur near the ball, broke my right tibia near the knee, fractured ribs 10 and 11 on my left side, suffered chest and possibly heart contusions, though my heart seems to be doing fine since the administration of some beta-blockers. This was all too much for the little hospital in McCall, so I was flown by plane to Spokane for my treatment. All the breaks had to be fixed surgically. I now have pins, screws, and plates in my left arm and right leg. My other leg and arm are just fine. Surgery went well and recovery seems to be going smoothly. I was brought home on Monday, though recovery will be a long and arduous process. Suffice to say, I’m done skiing for the season, and probably next season as well. I may be out for the hiking season this year, though by September, I could be up for some easy trails. It will be a few weeks before I can hold a camera, and a few months before I can walk.
In the mean time, I’m healing quite well and every day I’m getting stronger. So while there won’t be any new adventure stories from me in the near future, it won’t be long until I’m out and about again.
For Christmas, I bought Erin a new bird feeder to replace one that had been broken earlier in the summer. A few weeks ago, we finally got some seed and put it outside, but this was in the middle of a cold snap where daytime highs remained in the low 20’s, and the nighttime lows, well, we just won’t go there. For about a week, the feeder hung with no activity. Then, as the cold began to lift, there was a single chickadee in the lilac tree. It must have spread the news because a few days later, the feeder had full activity.
Erin had noticed that we had Chestnut-backed chickadees this year, in addition to the Black-capped and Mountain varieties that have been showing up regularly since we moved in. So, now we have three of the four chickadee species found in Idaho. It’s unlikely that we’ll see the Boreal chickadee at our feeders since it prefers high altitudes and is found in the northernmost portion of the panhandle.
Since the feeder has been up, we’ve also seen the return of the juncos, red-breasted nuthatch, house finch, pine siskin, and common redpoll.
One of the problems photographing chickadees is that they’re so damn fast. They would land on the feeder, and in the time it took to swing the mirror up and open the shutter, they were already leaving. I think the noise from the shutter/mirror mechanism is frightening them away. The result is very few images of chickadees sitting still, and a whole portfolio of chickadees in mid-wing flap. In some ways, this is no good, but in another way, it’s a neat series of images. So I present to you a gallery of chickadee mis-fires, or birds that just won’t cooperate for a photo shoot.
This week’s snowshoeing adventure takes us on thePotlatch Canyon loop trail (Clearwater NF #765). If the view above looks familiar, it’s because I have hiked this loop many times in the summer, and first posted about it two years ago. This time, armed with snowshoes, we had a very successful winter hike through the woods.
Despite the rising temperatures this past week, the Potlatch Canyon was still a veritable winter wonderland. In fact, I wouldn’t be surprised if the temperatures down by the water never rose above freeziing all day. That’s because we have been having some inversions the past week in which the cold air settles in the valleys leaving the high mountain elevations warmer than the lower elevations. Most nights, the low at the house gets down to less than 5º F while the daytime highs have reached almost 40º. In a place like the Potlatch Canyon, the inversion may stick around all day. That’s certainly what it felt like during our hike. It was quite cool along the river, and the entire time we were down there, the snow was fluffy and encrusted with the previous night’s hoar frost. When we left the river and ascended to the ridge, the temperatures rose and the snow turned into the wet and heavy kind that you usually encounter with temperatures above freezing.
When we arrived at the trailhead, there was another truck parked in the lot, but we never saw another person while we were on the trail. This left us with the feeling that we were in the middle of an isolated wilderness. The only wildlife we saw was a grouse, but we saw tracks belonging to deer, elk, moose, coyotes, snowshoe hare, and mice.
This trail makes for a relatively easy snowshoe. There’s not much elevation change, but be aware that walking five miles in the snow still takes more energy than hiking in the summer. The only obstacles to navigate are “downed” trees that are bent over due to the weight of the snow on them.
I’ve been spending a lot of time finishing up my dissertation proposal, which is due in a little over a week, and that has kept me from taking time to enjoy the outdoors. We got some considerable rain over the past weekend which lead to some dramatic skies and really clear views on Monday and Tuesday, but I just wasn’t able to take advantage of the nice conditions. I did get out for a little bit yesterday afternoon to check out the fall foliage in the arboretum on campus.
In Idaho, we don’t see very much fall color. There are a few shrubs and trees that turn this time of year, but for the most part, the grasses become even more brown, and most of the deciduous plants skip the color part altogether. The key to great color is a cold and wet climate. We have the cold during the winter, and even the wet in the spring and early summer, but it gets too hot and dry to sustain wild populations of maples, birches, and aspen. What we get are some stands of colorful trees here and there rather than large vasts of colorful forests that carpet the landscapes of Maine, New Hampshire, and Vermont. But there are some places where these trees have been planted and maintained in an artificial setting. The university’s campus is one place to find such color.
You won’t find much color out of the giant Norway Maples on the front lawn, but the Sugar Maples, Black Maples, and Red Maples along with a few other species produce spectacular displays. Some of the best fall trees are located right behind the life science building, but another great stand is found in the arboretum. These trees, native to northeastern North America, are sustained by constant watering and landscape maintenance throughout the dry summer. It’s the best we can do in this part of the country to reproduce the kind of fall seen in northern New England and southern Canada.
The fall colors that we know and love are a result of pigments produced by the plants year round. But during the growing season, they are masked by the abundance of chlorophyll produced. As a result, these pigments aren’t seen during the spring and summer. But as the season comes to and end and temperatures drop, the plant stops producing pigments for photosynthesis. The chlorophylls are the first to break down, and when they do, we are left with the xanthophylls and carotenoids which are yellow and red. These pigments aid the plant in photosynthesis by absorbing wavelengths missed by the chlorophylls. Each species has a different compositional make-up of pigments such that when the chlorophyll breaks down, we see different colors in each plant.
Click on the image above to see some more images from my walk in the arboretum.
A test shot from early on in the night. Notice the two meteors captured in this frame. Apparently, I also caught the end of a major meteor shower.
This story begins Friday night when I learned that a large coronal mass ejection (CME) sent a burst of solar radiation from the sun headed toward Earth. It was predicted to intercept our atmosphere on the evening of the 8th, producing auroral activity in the high latitudes. Given the size of this solar storm, as described by spaceweather.com, I was a bit suspicious that the auroras migh be big enough to see all the way down here in northern Idaho. So, I kept a watch looking for evidence of such activity.
On the evening of the 8th, I checked Spaceweather and confirmed that there had been some strong auroral activity, and that it had been seen earlier that morning as far south as Utah. I rushed outside and didn’t see much. I set up the camera for a test shot and picked up some faint auroral glow, but it seemed to be far in the distance and nothing worth getting excited over. I was beginning to think that I had missed the aurora and should have stayed up the night before. Throuout the evening, I would periodically go out side and take a test shot of the northern sky, and while the glow got brighter, it never reached the level that it had during previous auroras. So while I went out for the last test shot at 11:30, Erin had gone to bed. I stayed up in an attempt to finish grading exams, but ended up nodding off in the middle. I admitted defeat and around midnight, decided to quit and go to bed.
Curtains of light filled the sky during the most intense flare I had seen.
Before turning in for the night, I stepped out to check the sky once more. I figured, it wouldn’t hurt. Of course, I wasn’t expecting to see columns of light beaming high into the night sky. The aurora had really flared up. So I grabbed my jacket and my camera and decided to drive a few miles south where there were some flat fields and a clearer view of the sky. I was mostly interested in photographing the aurora with a different foreground than the usual barn and trees outside the house. When I pulled off the road and set up the camera, I got something I wasn’t expecting at all. There were full-fledged curtains streaking from the north across the sky overhead, and they could be seen clearly with the naked eye. This was too much to bear. I quickly set up the camera and snapped the first shot. Thankfully, there was cell service where I was and I was able to call Erin and get her out of bed for this one. I also called Colleen, who promptly got in her car and headed out to our place from Moscow.
Meanwhile, I stood out in the field for a good 20 or 30 minutes marvelling at the dancing curtains while snapping away. At one point, I noticed a flash in the sky. I thought maybe someone had come out with a spotlight, but there was no other human activity to be found. It happened again, and again, and soon I noticed that the light was radiating from the north and travelling toward me in waves. The activity persisted for a good 20 minutes and then subsided. At that point, the cold was getting to me, and I decided to head home rather than wait for Erin and Colleen to come out.
The last harrumph before fading away for the night. It was a much more quiet flare, but still beautiful.
The activity had subsided for a while, but I kept an eye on the reports from spaceweather.com. We went out again a little after 1:00 to see if the activity had returned, and indeed, the band across the sky had gotten brighter with some faint pillars streaking upward. Rather than drive back out to higher ground, we went into the field behind the house to see what was happening. The aurora certainly wasn’t as big as it was earlier, but it had gotten bright green. We waited to see if it would flare up some more, but it never seemed to get any bigger. So, by 1:30, we all decided to call it a night. Erin and I finally went to bed by 2:00, and after one last look at the sky, it seemed that the glow had faded out. Maybe the activity peaked again in the early hours of the morning, but I had already seen something good. After all, I had to be up in 3 hours to get ready for work.
While the lack of sleep had taken its toll on me, it was totally worth it to witness this totally awesome spectacle of the universe. A geomagnetic storm this strong doesn’t happen very often, and when it does, I’ll be sure to be outside capturing it.
Where have I been the last three weeks? To put it lightly, I have been choking on smoke. Since returning from the Seven Devils trip over Labor Day Weekend, the wildfires in the northwest, particularly in Idaho, have flared up. A fire south of the Devils appeared as well as a large fire just outside of Riggins. There have been some smaller fires near Grangeville and Lewiston to add to the mess. Winds from the south have blown all that smoke into the Lewiston-Clarkston valley and onto the Palouse where the smoke has been so thick at times, you could smell and taste it in the air and feel it in your lungs. Visibility has been cut to less than a mile. It’s been bad enough driving back and forth between school and home, and walking around town is miserable. My wife has had asthma flare-ups bad enough to warrant a prescription inhaler from the doctor. So with the air as bad as it is, I haven’t been out hiking or even photographing the local scenery.
Every couple of days, the winds might change, blowing most of the particulate matter out for a day or two, but it always returns. What we really need is a good storm to come through and not only blow out all of the smoke in the air, but put out the fires. Unfortunately, the long-range forecast calls for more dry weather which means the fires will continue burning. So until the air clears out a bit, it’s unlikely that I’ll be making any trips into the backcountry.
I went up to Freezeout Saddle with some photo club people to pick huckleberries. As I expected, they were still ripe, and very plentiful. But the problem with huckleberries is that you can pick for an hour and still not get very much. I think I came home with maybe a pint of berries.
I brought my camera up as well to get some photos of the area and of us picking only to find out that I left my card in the card reader and my extra card in the sack that I take backpacking. oops.