My Research: What I have been up to

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.

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4th of July

A Beargrass Mountain View

Once again, I missed the fireworks. I admit that I was looking forward to photographing them, but in the end, I was busy hanging out with friends, and we decided not to go over to Pullman. I did spend much of my nation’s birthday enjoying one of the best parts about this country: its wild side.

I went back up to Freezeout to hike into the alpine meadows of Grandmother Mountain, and I brought a friend with me who had never been up there. Our goal was not to reach the summit, but to simply escape the heat, enjoy the views, and see what wildflowers were in bloom. It was a beautiful day for a hike worthy of celebrating our day of Independence.

Wilderness is not uniquely American, but there are some unique aspects of the idea that originated here. There are many vast tracts of wilderness on the planet, but most of them are located in places that are either uninhabitable or are conomically depressed. But as third world nations develop and our resource consumption grows, these wild places are under threat of being lost forever. This happened through much of Europe where wilderness is nearly nonexistent. Sure, there are still natural places, but the habitat is highly fragmented and much of the forest land has been converted to fields for agriculture. The United States was headed for a similar disaster. Most of the forests in the east have been cut down at one point in our history and left to re-grow in small patches here and there. We have almost no original prairie left on the great plains. And the great western forests are logged down to the soil in places.

But before we could cut down every last tree and develop every last interesting place into a circus show, we decided that some places were better left unspoiled in their natural state, and that this untouched paradise could be an attraction in itself. So, at the end of the 19th century, the national park system was born, an idea that is truely American and has spread around the world in efforts to protect special places in danger of being lost for developmental gain. In the 1960’s, the push for true wilderness brought us the Wilderness Act of 1964, allowing congress to set aside land to never be developed. Few of today’s wilderness areas were untouched when designated, most were once logged or mined or farmed and were abandoned to be reclaimed by the forces of nature. This is what makes the United States so great and so unique. We are a developed and technologically advanced nation that set aside valuable habitable or developable land in order that we may have some wild places left to enjoy.

The forests of Marble Creek and Freezeout were once logged bare, but decades of non-use have hidden many of the scars. The landscape is beautiful up there with a sense that you truely are in a wild place, even if it’s not completlely untouched.

 

Grandmother Mountain Trail

I’m still amazed by how much beargrass is in bloom. It seems to be a good year. But all good comes with a trade-off, and the trade-off here is that the rest of the wildflowers don’t seem to be doing as well. The quantity of lupine blooming is down from the past two years, and much of the other color is missing as well. It’s not that the plants aren’t there, they just aren’t putting out flowers this year.

CJ and I hiked a total of four miles, two in and two back, which brought us up the slope to Grandmother Mountain, but not quite to the 6000 foot line. In other words, we didn’t make it to the big rock upon which I like to stop and rest. But that’s ok. I hiked four miles and my leg never bothered me. This marks the first time I’ve hiked that kind of distance since the accident, and to make it better, we made the hike in 2 hours, my normal hiking pace. I’m excited because I could very well be back to taking moderate day hikes by the end of the summer.

Mountain Heather and Lookout Mountain

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The Garden of 2013

Strawberries

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.

We have some tomatoes, peas, spinach, chard, and letuce growing in this box.

There's a tomato, spinach, peppers, lettuce, basil, and cilantro.

There’s a tomato, spinach, peppers, lettuce, basil, and cilantro.

 

This year, we planted a variety of squash and watermelon.

This year, we planted a variety of squash and watermelon.

 

Strawberry PatchStrawberry Beds

Squash Blossom

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.

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Aurora

The Northern Lights

Once again, the skies lit up with the dancing inferno of the northern lights. The sun has been fairly active the past two months, but this is the first I’ve both been aware of and had a clear sky to see. All of the aurora events I’ve photographed have been special, and each one is different. This one happened to be the strongest storm when the K-index reached 7. It was so bright, I could make out the red band with the naked eye once my vision adjusted to the darkness. The storm peaked here a little after 11:30 pm on Friday, June 28, sending columns of light high into the sky. After watching the display for nearly 40 minutes, I decided we should move to another location where the view of the sky would be a bit more open. Really, I just wanted a change of foreground scenery. We drove south toward the Bethany Chapel where we were at the southern end of a big, flat field. The sky was still glowing, but the streaks were not as bright. The moon had risen above the horizon providing some light on the foreground, but I also wonder if the moonlight was competing with the aurora. By 2:00, with no new major flares occuring, we packed up and headed home to go to bed. It’s a good thing we did, the storm had subsided quite a bit.

The Northern Lights The Northern Lights

This is the fourth aurora I’ve been able to photograph since moving to Idaho. Every time, I’m still amazed by the awe and beauty of this spectacle. I hope I never grow tired of enjoying these events. As we were driving to the Bethany Chapel, all I could think about were all the people we were passing who were totally unaware of the events transpiring in the sky outside their own homes.

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Evolution at Snowbird

Little Cottonwood Canyon

This year’s Evolution meeting was held at the Snowbird resort in the beautiful Wasatch Mountains outside of Salt Lake City, Utah. This year, I was fortunate enough to attend this meeting and present a talk on the correlation (or lack thereof) of boldness behaviors and swimming behavior in an open field. Of course, while meetings are great for presenting research from the lab, they’re also great for learning about other research and meeting people and making connections. This was my first trip to the Salt Lake City area, and despite staying at a hotel down in the valley, I really didn’t get a chance to explore the city or any of the surrounding area outside of Little Cottonwood Canyon. Nevertheless, I had a great time and really enjoyed this conference.

Evolution is generally held on the third weekend of June each year. This year, the meeting began on Friday, June 21 and ran through Tuesday, June 25. Barrie, Matthieu, and I drove down Friday morning, leaving here at 6 am and arriving at Snowbird right around 6 pm, just in time to catch the opening reception. Saturday and Sunday were full of talks, including my own talk on Saturday morning. I was so busy that I didn’t really have time to get out and explore. Luckily, they scheduled a half-day on Monday, giving us the afternoon off just for that purpose. I originally planned to hike from Alta over to Catherine Lake, but the road to the trailhead was closed. So instead, a group of us went up the tram and hiked from Hidden Peak over to Mt. Baldy, a short one-mile hike that descends 300 feet and then rises 400, both summits up around 11,000 feet in elevation. Unfortunately, Monday was the only day we had ovecast skies and rain. We managed to make it back to the tram before the storm really hit the mountain, but some others weren’t so lucky. A few hikers from LSU got stranded on the mountain when the tram closed early and had to hike back down in the storm. By Tuesday, I was fully exhausted, and after sitting through a morning of Quantitative Genetics sessions, I decided to take the afternoon off and ride the tram again to see the views in the sunshine. In fact, it was a great way to unwind before the final banquet. 

Conferences like these are exhausting. There were probably 2000 people in attendance and too many sessions to choose from. When picking out talks to see, there were often several I wanted to go to that overlapped at the same time. And it’s also easy to overload your schedule, which keeps you constantly on the move. By the second day, I had cut out all talks at the other building so that I wouldn’t have to keep walking back and forth. I also gave myself some breaks throughout the day. But even with this tactic, it’s still easy to become overwhelmed. In some ways, small meetings are nicer because there is only one talk session at a time and everyone is at it. On the other hand, there are lots of great opportunities to meet people and network. I’m exhausted, but I had a great time, and I’m looking forward to next year in Raleigh, North Carolina. 

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Palouse Falls

There seems to be a trend among people that when you live in a certain area, you tend to take for granted your proximity to tourist attractions and not visit them. Local attractions aren’t really a priority because they’re always there, so you can always visit them later. Well, later can turn into years. In this case, three years. I’ve gone three years without having visited Palouse Falls despite it being a major attraction in the area. To be fair, Palouse Falls isn’t really on the Palouse, but it’s an almost 200 foot sheer drop along the Palouse River in central Washington. It takes about two hours to get there from Moscow, and there’s not a whole lot else around it. Thus, it hadn’t been high on my priorities. Nevertheless, I’ve always wanted to see the falls, and I made an excuse to take Erin to go see them this weekend. To make the drive worth the effort, I planned to grab as many geocaches along the way as I could. I think I did pretty well: thirteen in one day.

So, here’s what makes Palouse Falls so special:

Palouse Falls - farther back

That waterfall is nearly 200 feet tall, 198 feet to be precise. If that’s not impressive enough, the falls are less than half the total depth of the canyon. Needless to say, this basalt gorge is pretty neat. The sheer canyon cliffs remind me of the sandstone canyons of southern Utah, at least in shape. It’s a very cliche western scenery. Somehow, there are trails that lead closer to the falls and even to the bottom, but with my leg still healing, I wasn’t about to risk an injury. So, we stayed in the safety of the canyon rim.

When I said that Palouse Falls was not on the Palouse, what I meant was that it’s not in the eco-region called the Palouse. The Palouse was a prairie, much of which has been raised for agriculture. It’s a region of lush rolling hills, wheat, canola, and lentil farms, and general awesomeness that looks much like this:
The Palouse

In contrast, there’s a point heading west where the farms end and the scrubby rangeland begins. It’s almost a desert out there with the main flora consisting of sagebrush and fewer grasses. It reminds me of southern Idaho, which is also a sagebrush steppe semi-desert with canyons cutting through the bassalt. I suppose that’s the real attraction. The landscape is beautiful. The towns are not. The nearest town to the falls is Washtucna. There’s a convenience store and a country dive bar. The rest of town is boarded up.

Despite its proximity to almost nothing, the park at the falls is pretty nice. There’s a well-kept lawn for picnics and camping and the trails are well maintained and easy to follow. I thought that the rainy weather would hamper my photography expedition, but I think I got a few nice shots with the wet camera. I’d certainly like to return in better weather, maybe even camp out to get some sunset and sunrise shots at the falls. I’d certainly like to hike down into the canyon once my leg gets better.
Palouse Falls Canyon View

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Spring Wildflowers and McCroskey State Park

When I started this blog, I never intended to make daily posts, but then, I thought that maybe I could come up with enough content to post more than once a month.

This month’s post is all about Spring wildflowers on the Palouse, because I’ve found some new ones and re-photographed some old favorites. To begin, I had realized that after three years of watching the Larkspur add a magnificent splash of purple to our yard, I had yet to put this plant in front of the camera. As common as it is, Larkspur might be one of my favorites simply because the deep hues are also extremely vibrant which makes this flower very noticeable even from a distance. So, let’s take a look at the larkspur:

Larkspur

Isn’t it wonderful? The purple creates such a nice contrast with the green grass, you can’t ignore it. And the best part of all this: it’s native. This isn’t some invasive exotic which usually colonizes disturbed areas such as yards. It actually grows wild here in the northwest. Larkspur is of the genus Delphinium. In case that name rings a bell, there is a cultivated Delphinium which really looks nothing like the D. nuttallianum pictured above. But then again, very few cultivated garden flowers resemble their wild cousins.

While I was photographing some of the larkspur, I happened upon four Camas plants, three of which are in bloom. During my first spring, I had been looking for Camas. After all, the Palouse prairie habitat closely resembles that of a Camas prairie. I first found Camas last year after hiking in the national forest. This year, the Camas seems to be everywhere. The four plants in my yard are a welcome find. I don’t know if I simply overlooked them in the past, or if this is the first time they have appeared on my little wildflower hill.

Common CamasBy the way, the Common Camas shown here is not the same as the toxic Death Camas. The bulbs of this plant are quite edible and have been collected as a food source by the native Americans and Lewis & Clark.

So far, this all seems great. I’ve finally photographed the Larkspur and discovered some Camas in the yard. You know what’s not so great? Trying to photograph these flowers. I’ve now been starting to walk for two weeks, but my leg is far from healed. I can bend my knee more than 90º, but still not all the way, and I surely can’t get into all of the positions I’d like to be in to photograph small flowers on the ground. It took some fancy maneuvering to get me on the ground only to find I was too close for my lens’s focusing abilities. I really do need a true macro lens for this work. I also can’t wait until I can properly kneel and roll around as needed for wildflower photography.

Ok, so that brings us to Sunday. I really wanted to go for a scenic drive with some geocaches to find along the way. Since it was already 2:00 before we were going to leave, I chose a route relatively close to home: Mary McCroskey State Park. This park is located just north of Potlatch in the mountains bordering the Palouse. The road through the park is named Skyline Drive. Like the more famous road of the same name, it’s a very scenic drive, but the similarities end there. This drive is unpaved and doesn’t contain pull-off overlooks. It’s not much different from a well-maintained Forest Service road. The route does wind its way through a mix of old-growth and logged habitats, and the abundance of wildflowers is nothing short of amazing.

At this time, the Trillium were at the end of their flowering stage and the Calypso orchids were out in full bloom. On parts of the drive, the bluebells were withering away, but in other locations, they were as strong as ever. In the midst of admiring all of the color, Erin noticed something new: a lily of fairly dull coloration with brown splotches. This flower was so camouflaged that I couldn’t even find it when we first stopped to look at it. This is the Chocolate Lily (Fritillaria lanceolata), and for all of its “dullness” on the outside, this is really one beautiful flower on the inside. Once we found this flower, we saw it everywhere along the rest of the drive. In fact, it may be the dominant flower in bloom on this day.

Chocolate Lily

Today was also Erin’s first sighting of Clematis in the wild. I had seen this flower before, but it was never in a pretty location to get a good picture of it. In fact, I thought the Clematis was a non-native, but I was wrong about that one. It’s just as native as the Larkspur.

As we made our way closer to the Palouse, the habitat and the floral communities changed. The cedar and spruce gave way to pines and the forest became more open and dry. The yellow flowers — Heart-leaved Arnica and Arrowleaf Balsamroot — became the dominant flowers. Shooting star became more common as well. The last surprise of the day was a Lupine in full bloom out in a clearing before we headed down the mountain to return home.

It was a great day to be out exploring and enjoying the landscape. It was a bit hazy to really enjoy the wide open views of the mountains and the Palouse, but there aren’t very many of those on this road anyway. The real gem is enjoying the flora and fauna of the forest. Later, when I can walk again, I’ll return and enjoy some of the many trails in the park and see what’s available away from the road. I’ll have to return anyway. I only logged two geocaches and there are more to be found.

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Problem Solving to Victory: RLE

Today I had a sort of “Boo-yah!” moment when I solved a problem I’ve been working on since the summer. Here’s the back story:

We’ve been integrating video tracking into our behavior assays in the lab, and in order to implement this method into research, I have been working with one of the math-bio undergrads on writing R-code to import and analyze each video, pulling out variables for statistical analysis later. We’re currently tracking fish swimming behavior in two dimensions from the side with the idea that we can add a third dimension with more cameras later on. We film the fish individually using a DSLR and use tracking software to extract the fish’s position at each frame in the video. The resulting data file outputs a video frame number, an x position, and a y position. From that data, we can pull out extra variables for analysis. For example, velocity can be estimated a number of ways, one of which is simply the square root of the change in x squared plus the change in y squared:

 v = \frac{1}{t} \sqrt{(\Delta x)^2 + (\Delta y)^2}

 

Once the velocities are calculated, we can analyze behaviors such as freezing, when a fish holds still and doesn’t move. Many fish will often freeze when placed into a new environment such as the filming tank. Some freeze for a long time before resuming activity, others may not freeze at all. After analyzing the freezing behavior in many many individuals, we can then run statistical tests to ask whether variation in freezing time is correlated with some other variable. But first, we have to define freezing. Because of the nature of tracking software, even when the fish isn’t moving, the tracking spot is, even if it’s ever so slight. This produces some noise in our data where the fish never actually reaches a velocity of 0. Therefore, we have to define a threshold where any velocity below that threshold is considered freezing and any velocity above that threshold is considered to be active. Here’s what happens when we simply define freezing below a threshold:

In this graph of Velocity over Time, the red dots represent velocities under the freezing threshold and green represents activity. Unfortunately, during the bout of freezing, some of the data points read as freezing. There are also a few points in the active zone that read as freezing. These points are where a fish reaches the wall of the tank and has to turn around. For a few frames, the velocity drops just low enough to be called freezing. Now, I could simply raise the threshold and solve most of the problem during the freezing bout, but I’d also get more freezing points when the fish is simply turning. Note the dilemma: How to isolate these few frames that are marked out of place and correct them.

For months, I’ve been pondering how to do this. I simply want to find a way to recognize streaks of data that mark True for freezing (or False) below a certain threshold streak, say 10 or 15 frames. In other words, any streak of True less than 15 frames should be turned into False, and so forth. Finally, last week I stumbled upon the rle() function: Run Length Environment. If you run rle() on a vector of categorical data (True, False), it will list every run length where the data are the same. So, for example: a data set that looks like this:

TRUE  TRUE  TRUE FALSE TRUE  TRUE  TRUE TRUE FALSE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE

will report the following with the rle() function:

Run Length Encoding
lengths: int [1:6] 3 1 4 2 5 1
values : logi [1:6] TRUE FALSE TRUE FALSE TRUE FALSE

So, great! Now I can identify runs of similar data. The only problem is, I need to identify which data points belong to each of those runs. After playing with it some more, I found that the output of rle() is simply a list, with $lengths and $values. So, make a new column in the data frame using the rep() function: rep(rle(x)$lengths,rle(x)$lengths). This tells R that I want to repeat the vector of run lengths, and each run length will be repeated the number of times as its length. Bear with me here. If the lengths were c(1,2,3,4,5), the output would look something like:
1 2 2 3 3 3 4 4 4 4 5 5 5 5 5. In fact, if you take the sum of rle(x)$lengths, you should get the total number of original data points. This new column of the data frame now associates every data point with its run length with respect to freezing. Now I can simply subset the data, finding all of the False where the run length is less than 15, and change it to True. Now I re-run the rep(rle(x)$lengths,rle(x)$lengths) and find all of the runs of True that are less than 15 and change them to False. And here’s the result:


Boo-yah! Problem solved!

Now I’m simply playing with different threshold values for both freezing and run length to get the most accurate freezing times. But now, I’ll not just be able to analyze freezing behaviors, but also swimming behaviors as a percentage of active swimming time, for example, time spent in different vertical zones. Of course, the number of variables to pull out of three simple numbers: x, y, and t(ime) is endless. But right now, I feel pretty good about solving this problem that’s been stumping us since last summer.

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Turnbull National Wildlife Refuge

I had to go to Spokane for a follow-up appointment with the orthopedic surgeon, and it happened to be a nice day, so I suggested that while we were up there, we should go to the Turnbull National Wildlife Refuge and spend some time outdoors. I’ve known the refuge was there and have always wanted to check it out, but I’ve always put it off. Since it has some handicap accessible trails, this was a good time to check it out.

Wildlife refuges are different than your typical national forest or national park lands. Their primary goal is to protect habitat for wildlife. Recreation comes second, which explains why most of the refuge is closed to visitors. Turnbull has some hiking trails, but not a large and extensive network of trails. These are good for gentle walks where hunting and wildlife viewing are the main objectives. The refuge itself is on a fairly flat landscape with an open savannah-like forest. It’s dotted with lakes and marshlands which bring in all kinds of birds. On this mid-march day, we saw lots of Ring-necked duck and American Wigeon, but not nearly the array of waterfowl down in Lewiston. I suppose we were a few weeks early since one of the lakes with a bird blind still had a significant chunk of ice over it. I also wonder if we would see more early in the morning. Instead, we hit the last few hours where the waterfowl were settling in for the evening and the songbirds were coming out for their last feeding of the day.

The refuge has a 5-mile auto loop with several small hiking loops along the way. Some of these are paved for disabled visitors such as myself, though I look forward to coming back when I can walk the other trails too. The refuge is a really nice birding paradise, and is also a good place to find moose and elk.

For more invormation, visit the official refuge page.

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Birding in Lewiston

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.

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The Ski Trip to End All Ski Trips

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.

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Chickadees

Chestnut-backed Chickadee

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.

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Winter Hike to Jerry Johnson Hot Springs

Jerry Johnson Hot Springs #2

Last weekend, I reported on a snowshoe hike along the Potlatch River and alluded to a second snowshoe adventure the same weekend. In fact, we had planned a little excursion out along Rt. 12 to Jerry Johnson hot springs. It turned out that the hot springs are still popular in winter, at least enough so that the one-mile trail was packed down such that we didn’t need snowshoes after all. So, for the second time this season, a snowshoe hike simply became a winter hike. While we were all looking forward to snowshoeing in, the real goal was to soak in the steamy pools beside the ice-cold creek, and in that regard, this trip was very much a success.

Warm Springs pack bridgeThe hike begins by crossing the Lochsa River over a pack bridge. Once on the other side, you walk through a beautiful forest along the banks of Warm Springs Creek. On this trip, it was a formidable winter wonderland with deep snow along the banks of the creek and sitting atop any rocks not submerged. There was a mixture of ice and free-flowing water, with some submerged ice clinging to the river bed. Make no mistake, this water was cold. In fact, we passed one family on their way out who had tried to jump into the first hot spring pool. At this pool, the hot water falls out of a cliff and collects along the side of the creek. During most of the year, the hot pool is either submerged or highly mixed with the creek water. The mother had undressed and jumped right in without testing the water first, and she received quite a surprise in doing so. The next pools were not much farther ahead, but it made no difference. The cold water was enough to send this family right back to the car.

In fact, the next pool wasn’t very much beyond the first one… maybe .2 mile or so. When we reached it, there were two families with children who were finishing up their soak. They told us that the third pool had been pretty trashed with beer cans and spaghetti-o’s littering the ground, but they had only heard that from the ranger. While they were getting out, I decided to go check out the third pool just to see what it was all about. It turned out that it wasn’t quite as trashed as the other people made it out to be and could have been perfectly good for us. This pool overlooked an open meadow with views of the mountains in the background and direct radiation from the sun. The only problem: it was lukewarm. So, we went back to the second pool which, despite its location in the shade, had the hottest temperature of any of the pools that day.

Winter WonderlandNone of the pools were extremely hot. The guide book says that the springs register at 115º at their source, but the pool felt like bath water. It was just hot enough to warm the soul, and cool enough to stay in comfortably for a few hours.

But what’s the fun in that? I challenged Tyler to take a little dip in the creek, so we walked down, wondering if this would be the end of us, and waded in. I’ve jumped into swimming pools straight from hot tubs before, and that’s enough of a temperature difference to cause some discomfort. But when getting out of a hot spring and stepping into (literally) ice-cold water, that just causes pain. In fact, I could only stay in up to my waiste for about 10 seconds before my legs went completely numb. Thankfully, there was a warm pool right next to the creek where we could let our feet thaw before getting back in the hot pool.

We were quite lucky to have the pool to ourselves. As we arrived, the families in the pool were drying off and packing up. There were two small groups behind us that went to the third pool. By the time we were ready to pack up ourselves, a few more groups showed up, and we passed some more coming in on our way out. So, really, we timed it perfectly.

Winter is the best time to visit these hot springs. Although they are still popular, they can get quite crowded in the summer, so you’re much more likely to have some extra space while there is snow on the ground. Besides, the hot water feels much better when complimented by a crisp winter day. I think another visit might be in store before spring arrives.

Trash on the trailNote: While the hot springs themselves were in pretty good condition, the trail was littered with beer cans and bottles. It was pretty bad to the point of causing aggravation. I’m not sure what goes through someone’s mind that makes it ok to just dump their trash in a nice beautiful setting, but if this is something you do or have done, please don’t ever do it again. Carry your trash out and dispose of it properly. It’s the only way we can continue to have beautiful and special places like this.

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Snowshoeing: Potlatch River Loop

View of the Potlatch River

This week’s snowshoeing adventure takes us on the Potlatch 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.

The Potlatch River Trail Duck Potlatch River

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Snowshoeing: Palouse Divide

Palouse Divide

I must have forgotten to post about this trip. This was last week, January 5, 2013. This was Idaho Parks and Recreation’s free day in which no parking pass was required to use the Park n’ Ski areas or any of the state parks. There are two Park n’ Ski areas near Moscow: Elk River and Palouse Divide. The Park n’ Ski areas are generally groomed nordic ski trails, but some of them are good for snowshoeing as well. Since the hike to Elk River falls would have been more than 2 miles one-way, I suggested we head up to Palouse Divide where a short trail would take us to a view over the St. Maries River valley. It would only be a mile to the view with the option to continue snowshoeing if we felt the trip was too short.

When we got to the snow park, I noticed that the first part of our trail was cleared for logging traffic. About .1 miles in, we found what looked like a nice trail that left the road and headed up, but that trail soon disappeared and after consulting the GPS, I decided that our real trail was up the road a bit. Of course, when we got there, we found that the entire trail to the Emida View was in fact plowed for the logging trucks. So, we had a nice walk along the road, but the snowshoes were unnecessary.

The views along this road are quite nice, and we had some special weather effects to make the experience a bit more magical. The first thing we notice are some snow-capped peaks in the distance, part of the St. Joe mountains behind St. Maries.  A little further down the road, the view opened up to the east exposing the rounded hills of the Palouse Divide. In the distance, we could make out the high peaks of the Freezeout Saddle area, but more immediately, Bald Mountain rose up as the highest point in the range. But here’s the cool part: In the valley, the mist had concentrated into a nice cloud below us. It’s a condition I have been waiting forever to photograph.

We ended up hiking well beyond the view, thinking that there would be an even clearer view up ahead, but eventually, we stopped for lunch and turned back. Since we didn’t get to use our snowshoes, I led a few people on a “short cut” off trail back to the parking area. While we had fun tromping through the 2-feet of powder, it turned out to be harder than we expected. Shadow figured it out with no problem. Greta kept getting stuck in some deep spots, though she eventually made it. Once we intercepted the old logging road, the rest of the hike was a breeze.

Palouse Divide seems like a nice place to explore the winter mountains of north-central Idaho, but either we’ll have to explore the other side which is not open to logging trucks, or cross-country ski it. This one seems like a better place to ski.

First view of mountains Emida View

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Snowshoeing: Spud Hill

Heading Down

This snowshoeing thing is taking off, and if I keep this up, I’ll be in shape enough to not suck at hiking at the beginning of the hiking season. This week’s adventure brings us up Spud Hill, also known by some as Mount Deary. Spud Hill was my first Idaho summit, and it’s a great little local hike that I often overlook. But I’ve always wanted to hike it in the winter, and today, Spud Hill became my first winter Idaho summit.

The one difference between snowshoeing and hiking, aside from the snow on the ground, is that distances seem longer than they would on bare ground. For example, during the last half-mile after we leave the main road, the trail switch backs and makes one last steep hurrah for the summit. Today, that section to the switchback seemed to go on longer than I remembered it. Perhaps its because each step takes so much more energy in the deep snow. On the other hand, that last steep ascent is much easier in snowshoes than in the summer when the loose gravel tends to give way under your feet.

In all, it was a great day. When C.J. and E.T. arrived at my house, they got stuck in the driveway and subsequently slid off the drive into the snow while backing down. We tried everything to get her car out, but evenually resorted to shovelling out a short path to the road behind her. That fun bout of problem sovling did cost us about an hour of hiking time. But no matter, we made it to the summit and back in about 3 hours.

The view from the top was beautiful. The Palouse was all covered in white, and the afternoon sun was golden. It wasn’t the clearest day, but sometimes, that makes the view more dramatic. The trees were still covered in snow, so it felt like we were exploring a winter wonderland. Then again, perhaps this part of Idaho is a winter wonderland. But see for yourself. Click on the image above to see more photographs from this hike.

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A walk in the snow

A layer of mist hovers over the snow behind the house.

A layer of mist hovers over the snow behind the house.

Well, now that Winter has finally arrived, we thought it might be fun to tromp through the snow and get some exercise. I dusted off the snowshoes (literally) and we set off for a little hike out of our back yard. As we began our trek, I noticed an awesome mist hovering over the snow, and since we hadn’t left the yard yet, we turned back to get my camera.

We were walking in snow that had not been disturbed, so it was quite soft and difficult, even with snowshoes. In fact, in the hour that we were out, we only managed to travel about .3 miles. Nonetheless, we had fun, and the dogs certainly enjoyed themselves. Greta loves the snow. It’s quite possibly her favorite thing all year round. When the snow accumulates, she become giddy like a puppy. She also likes to pretend she’s a wild dog by sticking her face into the snow as if to hunt mice running around beneath. Shadow also enjoys the snow. While she doesn’t quite act like a puppy, her favorite thing to do is roll around in it. It’s the first thing she’ll do, especially when we encounter summer snow patches in the high elevation.

Shadow shows off her beard of snow.

Shadow shows off her beard of snow.

Wild dogs, such as coyotes and foxes, are able to hunt even when the snow is six feet deep. Greta likes to pretend she is a wild dog.

Wild dogs, such as coyotes and foxes, are able to hunt even when the snow is six feet deep. Greta likes to pretend she is a wild dog.

By the end of our little walk, the sun had set and the mist had accumulated at the bottom of our neighbor’s field making a really neat scene. See some more photos from our walk below. Tomorrow, I think I’ll take the snowshoes out and explore some of the forest trails nearby.

The mist on the snow had accumulated at the bottom of our neighbor's field.

The mist on the snow had accumulated at the bottom of our neighbor’s field.

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Free Meat!

Warning! This post may contain some graphic and delicious images. Proceed at your own risk. Continue reading

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Thanksgiving, Parts II & III

Night Approaches

Las Vegas from Lone Mountain

Holy smokes, it’s almost Christmas and I never really finished posting about my Thanksgiving trip to Las Vegas. So, I’m going to give the abbreviated version of the rest of the trip and then move on to some more current events.

When I visit Las Vegas, it’s not for the usual reasons that most people go for. This is the second time I’ve been in the city, and I still haven’t been down to the strip or inside a casino. But it’s the second time I’ve been down there to visit TJ and Clare. TJ is one of my best friends from high school, and when we left for college, he joined the Air Force, so we’ve only seen each other a handful of times since then. It seems to be every two or three years for weddings, but now that our high school posse is nearly all married off, we’re going to have to come up with new reasons to get together.

TJ has the distinct advantage of living near the edge of town. That’s really an advantage for me for everything I love about Last Vegas is outside of town. He lives in the northwest corner only a few miles from a little desert oasis called Lone Mountain. This 800-foot hill has a few parks at its base where he and Clare like to bring their daughter to play on the playground equipment. There are actually tons of little city parks like these with picnic pavilions and playgrounds all dispersed throughout the city. But Lone Mountain also has a small piece of desert wilderness. The mountain itself is not technically a city park, but it seems to get quite a bit of recreational use. There is a trail to the summit where the view over the city is actually pretty nice. So on our first morning, we all went to the park. Well, almost everyone. Erin stayed back, not feeling very well. But Sophie and the dogs had fun playing on the jungle gyms.

Erin was feeling better later that afternoon, so we took a little drive that led us back to Lone Mountain. We decided to walk around the mountain a bit, and I was surprised when we actually made it all the way to the summit in time to catch the sunset. In hindsight, I would have brought a headlamp, but we managed to make our way back down in the dark just fine.

The next day, we headed out to Mt. Charleston to hike further out. Erin and I drove up to the Kyle Canyon trailhead on our previous visit, but that was right before TJ and Clare’s wedding, so we didn’t have much time to hike and explore. This time, we had their 2-year old daughter, so we wouldn’t be going very far, but this trip was more for the enjoyment of being out with friends rather than making miles. We ended up hiking a mile up the trail before turning back. Two miles for a two-year old is pretty good.

Kyle Canyon

TJ, Clare, and Sophie hiking in Kyle Canyon.

Aside from getting out and enjoying the warm sunshine, we had fun catching up while playing board games. I really miss having my game friends readily accessible. We played some Settlers of Catan, Alhambra, Ticket to Ride, Munchkin, and a new one for me: Mystery at the Abbey.

On Thanksgiving, Clare’s parents came over and we had a wonderful meal and too much food to eat. I would go back again just for the food. Sadly, we left Friday morning for the long drive home.

We took the first part of Friday’s drive pretty leisurely. The nice thing about this drive is that we got to see everything that we missed on the drive down. We drove the segment from Ely to Las Vegas in the dark. Once again, we reached Ely just after sunset, but I got to see a different part of the state. About an hour out of town, we stopped at at the Pahrangat National Wildlife Refuge to view some ducks sitting on the water. This is a neat spot where there are several natural lakes in the middle of the desert. It was also warm enough that I would have camped at the campground if I had enough time. We made one other stop just before reaching Caliente. I passed a sign for the Oak Springs Trilobite Area, and as soon as I saw it, I turned around to see what it was. There’s an area where shale containing trilobite fossils is exposed to the surface, and collecting is allowed. So, we took some time to find some trilobites. The majority of the fossils were only of the heads, so I collected no full-body specimines. But, these were my first trilobite finds, so I’m pretty excited.

The road beyond Caliente runs behind some of the highest mountains in the state. While we were at 6000 feet in the valley, Wheeler Peak in Great Basin National Park stood towering another 7000 feet above us. It was such a majestic sight, and even better to catch it just as the sun was setting below the horizon.

Sunset and Wheeler Peak

Wheeler Peak, Nevada’s second highest mountain, at sunset.

The drive from Ely to Twin Falls is really long in the dark. The road is very straight and the drive gets old fast when there is nothing to look at. It’s a full two hours to the next town, and when we arrived in Wells, I was really considering stopping for the night. I didn’t help that Erin wasn’t feeling well either, but I knew if I stopped, we’d have an even longer day of driving the next day. So, we continued on through, spending the night in Twin Falls.

It was also nice to see the scenery between Twin Falls and McCall during the daylight. The weather in Idaho wasn’t quite as pleasant as the weather in southern Nevada. It was cold, overcast, and for much of the drive, raining. This resulted in fewer stops which actually got us home at a decent hour.

This short trip has ignited my wanderlust. I really want to load up the car and just see the country with no real time limits and the freedom to just stop and explore on a whim. I also want to head south for the winter, but now that the ski season has arrived, I might just be willing to stay up north.

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What I am thankful for

During the weeks leading up to Thanksgiving, many people post about the things they are thankful for. I have been stewing over just how to say what it is I’m thankful for, because it’s a little bit different than most people’s ideals.

There are two major concepts that I am thankful for. Number one is free will. Number two is an objective universe. These two ideas are not unrelated. I am thankful to know that my thoughts, my actions, and my decisions are mine, and belong to no one and nothing else. At the same time, the consequeses of my actions are mine, and only mine to bear. I am my own master, and I am under no obligation to serve anyone else.

The thing is, the world is not a static place, and events happen outside our control that force us to make decisions that we don’t necessarily want to make. The thing is, these events aren’t inherently good or bad, we label them as good or bad depending on whether the outcome, or the effect, will be positive or negative on our lives. In fact, the same event can be both positive and negative at the same time. For example, your favorite team wins the championship game. That is good for you. You’re happy and joyous and generally in a good mood. Meanwhile, fans of the opposing team see this as bad. In reality, this event just is. It’s the outcome of a game where both teams played their best, and the winning team happened to play better on that night. We can find all sorts of causes to this effect after the fact, but we could only predict it from a known (or unknown) probability distribution.

When things happen to us, a common response is to say “It was meant to be.” It’s meant to be a statement of comfort. It’s the less extreme verson of “God wills it so.” But what does that really mean? If it was meant to be, then the world or universe (or God) intended it to happen. Intent implies cognitive will. Can non-living entities really impose intent? Does matter and energy really care what happens to you? If it was “meant to be,” then it was determined to happen from the start, and if that’s the case, we really don’t have any free will, do we? How is that comforting to walk around knowing that something out there is out to get you?

Instead, we can take another approach. This objective approach suggests that events in the universe are simply neutral. They have a cause and an effect, but they don’t happen specifically to target you. Instead, they are “good” or “bad” depending on what we make of them. When an earthquake hits a city, it’s not because some transient being wants to wreak havoc. It’s not to punnish people. It’s because the earth’s crust is broken into fragments that float on a semi-liquid mantle. These pieces move and crash into each other causing earthquakes and volcanoes that can set off other chains of events, and we just happen to be in the way. These events happen with some predictability as we gather data about our planet, but predictability does not translate into determination. Instead, there are tons of confounding variables that impede our ability to determine with 100% accuracy just what the oucome will be. Instead, we can predict a range of outcomes and their probabilities of occurance.

So what is it about an earthquake that makes it effectively neutral? For one, the earth’s crust is not a conscious being making cognitive decisions. Earthquakes happen wherever tension along naturally occuring fault lines builds up. This happens somewhat randomly and can occur away from centers of human activity. When this happens and no effect is felt, it goes unnoticed by the general public and can be dismissed as a neutral event. Of course, these very same processes that cause destruction and mayhem in our lives are the processes that allow us to be alive in the first place. If the earth’s  mantle were to cool down and solidify, the climate would change, our atmosphere would collapse, and life would cease to exist.

Of course, I’ll stop here because, as it turns out, Neil DeGrasse Tyson can explain the objectivity of the universe a lot better than I can.

To me, this idea of a random and objective universe is a lot more comforting because I know when things happen, it’s not specifically directed toward me, and all I can do is choose to dwell in the negative or find the positive. And for that, I am thankful.

Oh, and also for my wonderful wife.

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