Sunday, June 30, 2013

L. Beckman HJA Week 1

9:10 pm 06/24/13 Quartz Creek Building HJ Andrews HQ
To Whom It May Concern,
            Lo! I hath begun my four-week quest to achieve scientific success at HJ Andrews Experimental Forest. Let us explore this majestic Northwest forest together, with the triumphant and cascading symphony of science echoing in our minds!
            We began our journey by meeting the collegiate students, the USFS researchers, and the HJA scientists. Charles Halpern guided us all from this to a quick tour of the labs to a checkout of equipment. Once we were suited up, we loaded up our vehicles and sped off to Bunchgrass Ridge. With a spirited gusto we hiked around and perused the study areas, identifying a multitude of flora and fauna on the way. The time sped past as we were taught the basics of the research plots and transects. Just when, mind could not take any more information, we concluded our trip and traveled back to camp. We had successfully concluded our first work day.
            I look forward to the next four weeks with the promise of intellectual pursuit, scientific progress, and personal achievement. I conclude this journal entry with a quote from William Mathews: “A great deal of the joy of life consists in doing perfectly, or at least to the best of one’s ability, everything which he attempts to do. There is a sense of satisfaction, a pride in surveying such a work—a work which is rounded, full, exact, complete in it’s parts—which the superficial man, who leaves his work in a slovenly, slipshod, half-finished condition, can never know, It is this conscientious completeness which turns work into art. The smallest thing, well done, becomes art.”
Liam Beckman

8:58 pm 06/25/13 Quartz Creek Building HJ Andrews HQ
To Whom It May Concern,
            The second day is done and we are furthering our botanical skills and expertise. We focused on plant identifications during work today, especially in regard to grasses and other “hard to ID” plants. I have a lot to learn but I am surrounded by very bright and very kind men and women. It has been great to work alongside people who live and breathe biology as it serves as a tremendous source of inspiration. We also centered our efforts around plant cover estimations. In order to maximize the accuracy of findings/data, we need to calibrate our estimations relative to one another. It is of great relief to find that this is not a harsh or cold effort, but rather a team-effort enhanced by supportive research members. The greatest challenge so far is the sheer quantity of facts and knowledge needed to succeed here. Yet with a persistent and focused effort, I am confident that such a challenge is achievable. Furthermore I know that if I am able to play with science as a friend, and simply work with science as a colleague, I will have achieved success. I conclude this journal entry with a quote from Stanley Hall: “Play is pleasurable mental and physical competitive exercise where the issues involved are trivial and transient. It is a fit preparation for more important tasks. And it is the law of life that you only do these things well at which you have played in childhood.”
Liam Beckman

9:01 pm 06/26/13 Quartz Creek Building HJ Andrews HQ
To Whom It May Concern,
            A torrential downpour soaked our jackets, slowed our progress, and soggied our dispositions. Fortunately, I avoided the latter two with a thermos of warm tea. Charles was unable to accompany us today sue to prior arrangements. As such, the role of leader fell on several talented collegiate team members. We continued our work with quadrants both in identifying plants and estimating plant cover. We calibrated as a whole team today, with some hit-and-misses. We will later calibrate with Charlie to confirm our estimation paradigms. Today’s rainstorm drove us back to HQ several hours early, where we then continued research under the lab’s dry roof. Despite and present challenges, I feel confident that our collective skills are increasing.
 HJA Day is tomorrow, and I look forward to partaking in the activities, as well as catching up with my readings. I close this journal entry y with a quote by Emerson: “The power of a man increases steadily by continuance in one direction. He becomes acquainted with the resistances and with his own tools; increases his skill and strength and learns the favorable moments and favorable accidents. He is his own apprentice, and more time gives a great addition of power, just as a falling body acquires momentum with every foot of the fall.”
Liam Beckman
9:00 pm 06/27/13 Quartz Creek Building HJ Andrews HQ

To Whom It May Concern,
            HJA Day was really-jam-packed and educational. We began by rotating around four stations
1.      Stream/Light Temperature Dynamics
2.      “Ellie’s Log” Author Interviews
3.      Spotted Owl Population Studies
4.      GREENhouse Exploration.
I especially enjoyed the artwork and themes of “Ellie’s Log”. Ms. Li stated that she wished to inspire 8-12 year olds to pursue science and explore the outdoors—a very admirable goal. For myself, a large portion of my interest in science stems from my time in 3rd-5th grade with wonderful teachers.
            Later, I embarked on a field trip to a down-log/decomposition site. The rip leaders had us observe the forest and write about our impressions. They explained the 200-year ecological experiment centered around decomposition and artistic expression. Established in 1982, this project aims to bring together a long-term, comprehensive analysis of specific forest dynamics. The addition of writers makes it a rather unique experiment.
            Tomorrow, Wirt, Magee, and I will have a longer day because we will work with the Hummingbird Catching Crew. I look forward to this new opportunity. I conclude this journal entry with a quote by L.M. Alcott: “Far away there in the sunshine are my highest aspirations. I may not reach them, but I can lookup and see their beauty, believe in them, and try to follow where they lead.”
Liam Beckman

8:38 pm 06/28/13 Quartz Creek Building HJ Andrews HQ
To Whom It May Concern,
            today served as a great day to conclude the working week—a 14 hour day with 3 different crews and with the first sweltering day of our time here. Magee, Shannon, and I spent an hour with the hummingbird catching crew, 10 hours with the Bunchgrass crew, and an hour with the songbird catching crew. Our time with the bird crews was especially interesting as we got to observe their species up close.
            We collected love data for the first time while at Bunchgrass Ridge. My partner, Betsy, and I completed plant-cover estimations for three subplots with four 1x1 meter quadrants each. It was tough work and drained me mentally and physically, but Betsy stayed positive and supportive the entire time. I plan to continue my reading and exploration of the surrounding area over the weekend. I conclude this journal entry with a quote by Leigh Hunt: “There are two worlds; the world that we can measure, with line and rule, and the world that we feel with our hearts and imagination.”
Liam Beckman

8:09 pm 06/29/13 Quartz Creek Building HJ Andrews HQ
To Whom It May Concern,
            I centered today around reading and general recuperating. I continued my studies with biology and introduced myself to cellular respiration and other cool biological systems. I was wondering just how plants know sunlight shines on them? Furthermore, when they know, what actually happens? My biology textbook (Biological Science, Scott Freeman, 3 ed., p. 859) answered both questions relatively easy. What happens is a multistep process that begins in the cell (in the case of sunlight shining on a plant, this process starts with a receptor cell). When sunlight hits a plant, a receptor protein in a receptor cell changes its shape in response to this external signal. This allows the protein to catalyze a chemical reaction—a phosphorylation reaction. This reaction either continues down in a phosphorylation cascade or releases a second messenger (typically calcium ions). In either case, there are three endgames before the signal leaves the cell:
1.      A specific DNA segment is activated or repressed in its transcription;
2.      mRNA, tRNA, and rRNA proteins are activated or repressed in their transcription;
3.      A channel or pump has its ion flow changed.
In all three instances, the receptor cell generally then releases a hormone, or a cell-to-cell messenger, to other cells. These internal receptor cells translate the hormone into a message that then changes activity within the plant (in the case of the sunlight, the internal receptor cells may tell the plant to grow toward the sun).
 Tomorrow I plan to explore the terrain and begin our final project with the poster. I conclude this journal entry with a quote by James Russell Lowell: “Solitude is as needful to the imagination as society is wholesome for the character.”
Liam Beckman

14.5 Hour Day: Hummingbirds, Bunchgrass Ridge and Mist Netting

Because of scheduling issues, Shannon, Liam and I ended up going along with three projects on Friday.  This made for a long day, but I think that it was worth it.  Especially considering that we will not have the chance to see some of this work later in the Summer.

Catching Hummingbirds

At 5:30 AM, we went behind on of the apartments to observe the hummingbird project.  Hummingbirds are caught, measured, tagged, and released to get an idea of the biodiversity.  I think that some of the data might also be used for phenology.  This is part of the Hummingbird Monitoring Network. We were working with Sarah and Adam Hadley.  They have some great photos and information on their blog.  For example, I just learned that "Rufous hummingbirds (Selasphorus rufus) are declining at a rate of nearly 3% per year."  The Hadley's also work with hummingbirds in Costa Rica.

 Five hummingbird feeders have been set up for a while.  On the day of the collection, three of the feeders are taken away, while the other two are mounted under a trap seen in the background.  The trap looks like an upside down crab trap.  When the hummingbird approaches the feeder, the research team allows the birds to drink a little to maintain their energy and then they release a string that drops the trap.
 Once the bird is trapped, it is easy to reach in and collect them as Adam is doing here.
The tiny hummingbirds are put into a net bag like this and lined up in the order that they have been captured.
Sarah takes measurements of the birds including length, feather length and condition, weight, gender, the amount of fat they are storing in a pocket near their neck, and whether or not they are carrying eggs.

 Here is the rufous hummingbird with it's tail flailed out.  They also put little tiny leg bands to identify the birds if they are ever recaptured.  I wish that I had a close up to show how small they are.
 Once all of the data is collected, the birds are force fed a little bit more sugar water and then they are set free.
I am releasing one in this picture.  It was in my hand a split second before the photo was taken.

Here are a couple more waiting to be measured.

Bunchgrass Ridge
Between 6:30 AM and 5 PM, we did our work on Bunchgrass Ridge.  Today was our first day of actual data collection on Bunchgrass Ridge.  I'm finding myself getting more comfortable with the plant ID.  In fact, now that I am home fore the weekend, I have been able to walk around my yard and notice some of the diversity of weedy-looking plants that I have growing here.  I will describe the field protocols in more detail later, but here is a brief overview:

We start by laying a transect diagonally through the 10 m X 10 m subplots. 

 Within that transect, we observe four quadrats at predetermined distanced along the transect.  This is the first quadrat that Zach and I measured on the first day.

Within the quadrat, we identify what species are present and measure the percent cover that each species represents within that 1 m X 1 m square.

My partners and I were able to get through 3 transects with 4 quadrats each.  Eventually, each person should be able to get through about 16 quadrats by themselves per day.  It was about 8 hours of standing in the sun counting plants.  Charlie has been telling us to take it easy if we find ourselves beginning to get exhausted.  The data is no good if we our tired and not paying attention to detail.

Mist Netting for Birds

From 5-7 PM, we went out to mist net for birds.  This was similar to the hummingbird project.  The birds are collected, banded, measured and released.  Their poop is also collected to see what the birds have been eating.  

A mist net is placed in a corridor between the trees.  One researcher sits in the bushes and plays recordings of the territorial songs of the different birds that may be in that area.  When the real birds come down to defend their territory, they become tangled in the mist net.

 The researchers must carefully remove the bird from the net.  I think that this is a chestnut-backed chickadee (Parus rufescens).  It got itself really tangled in the netting.

 It's fun to see the mass measured since the birds just sit upside down in a small piece of PVC tubing.
 The poop is collected in a small bottle of preservative and sent back to OSU to be analyzed.  The undigested mandibles, legs, and other insect parts and counted to see what the diet of the birds has been.  I guess that the birds will always poop after they have been left in a dark box for a few minutes.

 Here is a Dark-Eyed or Oregon Junco (Junco hyemalis).
 Liam got to release the junco.  Many birds will lay still when placed on it's back.  When traveling with animals, my partner Jennifer and I once traveled several miles with an African grey parrot laying on the dashboard of the van.

With a little prompting, this junco eventually flew away.

At the end of this long day, I was able to enjoy some leftover lasagna and homemade pizza with the people from my bunchgrass team and my roommates from the team studying pollinators.  Fruit and barbeque sauce pizza stood out to me, but the sweetened condensed milk pizza was my favorite.


Other pictures from the first few days

Here are some pictures that I could not post earlier because I forgot the connector chord for my camera.  They are from the first week of field training and from HJA Day.

Liam and Shannon eating lunch on Bunchgrass Ridge


Meadow on Bunchgrass Ridge

Western Toad (Bufo boreas).  We saw a big adult too, but I didn't get a photo.

Butterfly, yet to be determined

Northern Alligator Lizard (Gerrhonotus coeruleus)

Shan with the Alligator Lizard

The inflorescence of a carex grass

Sorting grass in the lab

Setting insect pitfall traps the day before HJA Day

Liam and Shannon examining a trout

The RET group discussing ways to do insect collecting with students.  Pitfall traps, and beat sheets.

Malaise trap for flying insects

Emergence trap for insects flying out of the water

Examining the captured insects with Judy Li

This is really cool.  Bird poop is collected from little birds.  The birds poop when they are in a dark box.  The poop is sent back to OSU and analyzed.  An expert looks through the poop with a microscope for undigested insect pieces and determines the diet based on that.

Friday, June 28, 2013


I went for a hike today.  I was told that the trail I was on was not great, but it was good if I wanted to just move around a little.  It just follows the creek.  It was fantastic.  The trail let through several different stands of old-growth.  There were big old trees, and big dead trees.  There was varying amounts of light coming through the various layers of canopies caused by the big old trees becoming big dead trees.  As I was walking, I was thinking that if this trail isn't even one of their good ones, than there must be a lot of really great trails here.

Today was HJA Day.  This is a day for people to learn about all of the different projects that are being done in the experimental forest.  A lot of people came in from OSU, Willamette University, Forest Service, and many other organizations.

Here are some of the researchers discussing the project here at HJA:

Dr. Dana Warren talking about his work on connections between canopy and stream ecology

Dr. Judy Li discussing her children's book, "Ellie's Log" about doing science in the field 
(the audio is a little quiet.)

Dr. Mark Schulze, HJ Andrews Forest Director, discussing the phenology research at HJA

Dr. Steve Ackers discussing his work with spotted owls

Mark talking about the GREENhouse project here at HJA

Here is the eventual in-wall house data center
This is the GREENHouse
The house is has triple pane windows and the molding is all made from logs that fell here at HJA.
Here is one of the monitoring sensors in the wall

Ventilation System
One kitchen
Another kitchen

 Mark describing why we wear hardhats

 In the afternoon, we went into the field.  These former RETs and Kari and describing how to make pitfall traps and use them with high school students.

 This is a description of the forest wireless network that they have at HJA.  This allows researchers to stream continuous data from the field or check their email.  The WiFi is called "Big Tree 1," "Big Tree 2," and "Big Tree 3."  This is because the wireless is attached to big trees.
And then I ran into former Sandy High School student, Will L'Hommedieu.  He is now a PhD student at OSU Forestry studying the movements of small woody debris in creeks among other things.  
I am starting a relationship with the Swainson's Thrush, Catharus ustulatus, outside my window.  Every morning at about 5 AM, it start going "Tweedle-dweedle-dee."  It reminds me of the rooster that I knew in Ranomafana, Madagascar.  The rooster lived on the hillside opposite of my tent.  It had congestion in it's throat and every morning, it was say, "cock-a-doodle BLEGHTH."  Eventually, I grew to enjoy the rooster saying, "good morning."  Maybe, I will eventually grow to appreciate my window friend that begins my day an hour before necessary.

Wednesday, June 26, 2013

First Few Days at H.J. Andrews

Oops.  The date is off by 100 years

We are finishing up our third day at HJ Andrews LTER (long-term ecological research) Experimental Forest.    As part of the Research Experience for Teachers program, I will be working with a researcher studying the disturbance ecology in a forest/meadow ecosystem.  The research area at Bunchgrass Ridge has been a open meadow ecosystem for a long time but it has been invaded by tree species.  The principal researcher is Charles Halpern and he has a team of several students and two forest service employees.  The research is looking at the changes in plant diversity after the removal or burning of trees.  I have two students working with me, Liam and Shannon.

The first few days have involved learning lots and lots of plants.  Most of the plants are plants that I have probably passed thousands of times without a thought.  It is exhausting to learn all of the plants.  I am getting to know the anatomy of grasess, and the differences between asters, the difference between rubus and ribes, and many scientific names. Some things are ranunkulus.  We have also done a few practice plots and calibrated our observations.

I'm also getting to know all of my new roommates.  My roommates are my students and a group studying flower pollinators.  There is one studying log jams.  He doesn't live with us but he is here most the time.  So I guess he lives here.

In the other building there is a team looking at spotted owls and another one tracking birds through bird calls.  Those are just the teams that are here now.  There is much more happening.  Tomorrow is HJA day.  We will get to learn about all of the projects.

It has been raining like crazy for the first few days.  I have some camera pictures of us all sopping wet, but I don't have my camera cord.  I will put them up when I can.

.pdf of some of our plants that we are working with and learning to identify.

I have been trying to eat as many of the plants as possible while we are studying them.  I think that the ones that I eat are the ones that I am learning the fastest.  Calochortus subalpinus has a bulb that can be eaten raw or collected and roasted over a fire.  But the flower is very beautiful so you should avoid picking it if possible.  I pulled up some thistle root but forgot to eat it.  Vanilla leaf (Achlys triphila) can be dried and hung in the house to repel bugs.  Wall lettuce tastes like bitter lettuce and its scientific name translates to "lettuce wall."  Arianna from our team also pointed out that grand firs (Abies grandis) taste like Christmas and douglas firs (Pseudotsuga menziesii) tastes like Portland.  I'm not sure about the taste of Portland, but they definitely taste different.

I also learned about machine learning.