Tuesday, August 17, 2010

'10 REUs Say Goodbye to Harvard Forest, For Now

By Aleta Wiley

After their two-day Symposium and a final day of cleaning, organizing, and packing, the summer students at Harvard Forest had nothing remaining except to say their goodbyes before heading back home. For twelve weeks, the students lived together in two houses at the Forest, sharing stories about their homes and colleges, from Oregon to Texas to Wisconsin to Vermont. Now, it was time for them to disperse and begin telling their friends and family the stories about their summer in Petersham, MA. Thank you all for a fantastic program! Keep in touch, as all of our paths are bound to cross again in the future.

Friday, August 13, 2010

Student Highlight: A Final Excursion Before the End of Summer

By Sarah Gray

Before tears were shed and goodbyes were said, a few of the REU students went for ice cream at Carter and Stevens, a local farm store.

C&S is famous for their Friday night cookout, where they serve burgers, corn, and fresh veggies roasted over the fire.

With none of Tim's delicious cooking at Harvard Forest and no reason to buy groceries since everyone was headed home the next day, a few of us went to chow down on locally-produced beef and delicious grilled veggies.

The evening ended with eating fresh homemade ice cream, feeding the cows, and playing on the swings. It was a low key event - a wonderful and relaxing way to spend our final Friday night together.

Thursday, August 12, 2010

REUs Ace Summer Symposium!

By Aleta Wiley

In the final week of the Summer Research Program in Ecology for Undergraduates at Harvard Forest, all 33 students participated in the Student Symposium on August 11-12 in the Fisher Museum. Over a day and a half, all the students presented 15 minute talks to an audience comprising program mentors, university professors, Harvard Forest researchers, family members, and of course, their fellow students.

As each student discussed his/her summer research, the audience was impressed with the diversity of projects presented (Abstracts are available here). Since Harvard Forest is an LTER (Long Term Ecological Research) site, several students had continued large-scale research projects that have been operating for several years. Two students collected and analyzed data from the Hurricane Plot, an area of experimental forest that sustained a “simulated hurricane” 20 years ago in order for researchers to learn more about the effects of wind disturbance on the land. Other students conducted research on the “soil warming” plots designed to learn how climate change might affect the environment. Two other students monitored woodpecker nests in suburban and natural environments, continuing observations that have been made for 5-6 years.

Not all projects this summer had been long-running, however. Several students helped with experiments that were in their first year, but that are expected to continue long into the future. These students learned a lot about the value of collecting baseline data so that future researchers will be able to detect changes in their plots.

Still other projects addressed more computational and technological advances in the field of ecology. One student used GIS to study distribution of an invasive species; others placed cameras on forest towers to detect changes in phenology, and another student developed models and simulations to learn about climate change.

Two students represented the social sciences and presented results from a survey distributed to 1,000 landowners in Vermont and New Hampshire. And, another student produced a documentary film about paleoecology, which, among other uses, will be incorporated into the Harvard Forest Schoolyard Ecology program, where local schoolteachers introduce ecology research in their classrooms. (Watch the video on YouTube here: "Secrets of the Mud: A Hemlock Mystery".)

As the Symposium concluded on Thursday afternoon, the students released cheers of excitement as they recognized how much work they had accomplished over the summer and how their time together was quickly approaching an end. A celebratory barbeque was prepared by our ever-hardworking cooks, and the Summer Program came to a close over a beautiful New England evening.

Tuesday, August 10, 2010

Harvard Forest Get-Together at the ESA Annual Meeting

By Aleta Wiley

This year, Harvard Forest organized a social event at the Annual Meeting of the Ecological Society of America in Pittsburgh, PA. The goals of the social were to bring together past and current folks who have worked at the Forest to catch up with each other and to provide an occasion for any undergraduates attending the ESA Meeting to come learn about opportunities at the Forest.

On August 3, 17 people attended the social at Olive or Twist, a martini bar close to the Convention Center in Pittsburgh. 7 past REU students, 5 past researchers, 4 current researchers, and 1 potential future REU student were able to connect with each other, chat about current projects at the Forest, and learn about how Harvard Forest has influenced their lives and career paths. It was great to learn that several REU alumni have attended or are now enrolled in graduate ecology programs around the country!

Thanks to everyone who attended this event – we’ll hope to see more Harvard Forest alumni in the future!

[Morgan Tingley (REU '00 & '01), Sarah Butler (current researcher and mentor for REU program), and Jen Johnson (past research assistant) chatted about current projects at the Forest]

[Marit Wilkerson and Jens Stevens, both REU Alumni from '05, caught up with each other while discussing the benefits of the Harvard Forest program with Ava Hoffman, an undergraduate at the University of Virginia.]

[Naomi Clark and Matt Lau, both REU alumni from '03, were excited to re-connect at this event]

RESEARCH PROFILE: Using Models to Project How Climate Change Might Affect Oak Species Distribution

By Elisabete (Baker) Vail

Imagine if crystal balls which allowed us to catch a glimpse of the future, actually existed? What would you use them to see?

Well, in a way – they do exist. In the abstract world of math and computers, “models” are fed datasets of current day information and asked to project future outcomes. Ecologists use them to forecast how current events will shape our future planet. This is what I have spent my summer, attempting to do.

My project attempts to project the possible affects that increasing climate change may have on oak species distribution. Focusing on 27 oak species, located across the eastern United States – I am using information collected for over 81,000 sites from both current day Global climate models and future emission scenarios to predict what the region may look like in the year 2050.

In order to do this, I spent the majority of the summer using an open-source (free) programming language called R to write dozens of computer programs, which allowed me to organize this collection of information into three datasets – present day, future emission scenario 1 and future emission scenario 2. These datasets, which basically look like giant excel sheets, are divided into rows representing site locations described by latitude longitude (over 81,000 rows) and columns representing presence absence data for each of the 27 oak species and relevant environment variables for the given location. In the future emission scenarios datasets, the presence absence data was omitted, because this is exactly what we are trying to project.

I then analyzed the initial present day data using a statistical model, creating 27 new sub-datasets containing presence absence data for a given oak species and the top 5 environmental variables most relevant to that species survival.

These new datasets, along with both of the future emission scenarios were fed into an ensemble suite of 9 separate statistical computer models. Maps were produced from these models, for the eastern United States, showing both current and predicted presence absence data for a given oak species.

This was an amazing project to be part of. In the last few months, I have learned a great deal about the concepts of computer models and the extreme importance of validating the accuracy of our data. I have also fallen in love with programming and developed a strong sense of confidence in not only my abilities as a computer programmer, but also in the role that my skills can play in current day science.

My project was really just a small part of a much larger goal, which will continue on without me. In the future, my work will be used as a reference against a new improved statistical model currently being developed by my mentors. I’m sad to leave Harvard Forest and the work that I have done here, but am comforted in knowing that my work will go on to become a part of “real science”. It is truly one of my greatest academic accomplishments and I am so grateful to have had this opportunity.

[Elisabete (Baker) Vail is a senior at Simmons College in Boston, Massachusetts and will complete her double major in Biology and Computer Science this December.]

Monday, August 9, 2010

RESEARCH PROFILE: Vegetation Sampling in Wildlands and Woodlands

By Maddy Case and Joe Horn

We have spent most of the summer traveling across New England to do field work at sites in Massachusetts, New Hampshire, and Maine. At each site, we have been establishing permanent vegetation sampling plots for a long-term study comparing forest dynamics in managed and unmanaged forests. We carry 2-foot pieces of steel pipe into the woods (3 lbs per pipe x 3 plots x 4 pipes per plot + 10 lbs for other gear = Wicked heavy), use them to mark the corners of 20x20 meter plots, and survey these plots for herb-layer species, saplings, trees, evidence of historical disturbance, and environmental variables. Over the course of the summer, we have gained familiarity with the flora of New England and cemented a great friendship while also learning about the logistics and challenges of independent field research.

A typical day in the field would involve sampling 1-4 plots, depending on the difficulty of access and sampling. The two sites in Maine proved the most challenging, what with fir-choked stands and an abundance of new species to learn in Dover-Foxcroft, and long hikes through recently logged forests and vicious spruces in Amherst. In all, we sampled about 60 plots this summer (roughly 6 acres of forest in total!). On the rare days when it rained, we rejoiced and worked on data entry and identifying unknown species.

Since returning from our last field excursion, we have spent the last two weeks of the program focusing on our individual projects for the symposium. Maddy is analyzing the data from the past three years of W&W vegetation sampling to study the effect of overstory composition and environmental variables on understory diversity. Joe is working on improving data management and creating a master species list for the project. After spending half the summer camping, cooking for ourselves, and regularly confronting insects and humidity, we are enjoying our beds, Tim's cooking, and the chance to work inside unperturbed by the weather.

Wednesday, August 4, 2010

PROJECT PROFILE: Exploring the Abiotic and Biotic Drivers of Soil Respiration on the Harvard Forest Prospect Hill Tract

By Claudia Reveles, Joanna Blaszczak, and Maya Thomas

Our project is in the field of soil carbon dynamics, specifically looking at the rate of carbon dioxide efflux around Prospect Hill as well as areas that have been manipulated by different abiotic (nitrogen input and temperature) and biotic (adding leaf litter and removing roots) factors.

A preliminary map was generated using GIS to identify areas (polygons) in Prospect Hill with unique stand (prominent tree species) and soil drainage types. A total of 59 areas were identified, but some were excluded due specific conditions (i.e. excessively drained areas like bogs and impervious areas), leaving a total of 56 plots. The biggest polygons have three plots each. For reconnaissance, we used GIS to find the center point of each polygons on, and would place a collar down for the sampling chamber to be rested upon. We also sample at four different treatment areas: trench plots, chronic N, and soil warming (hot plants/warm ants), all located in the Prospect Hill tract, and DIRT (detritus input and removal treatments), which is located in the Tom Swamp tract. At the trench plots, a tarp was placed underneath the area and the roots were removed. At the chronic N plots, we sample six treatments, low nitrogen input, high nitrogen input, and control in both a pine and deciduous stands. The soil warming site has 30 plots with varying temperature changes. There are 21 DIRT plots, some with double leaf litter, others with the O and A soil horizons removed, and other such manipulations. We placed three collars in each DIRT plot and five collars in each chronic N plot. There is one collar in each of the soil warming plots, and three collars in the trenched plots and three collars outside of the trenched plots, which serve as the control.

We have divided tasks among our group, with Claudia dealing with gradient (Prospect Hill) efflux trends, Joanna looking at trends among the different treatments, and Maya conducting spatial analysis to look at efflux trends based on location in Prospect Hill. Soil respiration, as well as soil temperature and soil moisture, is measured every week, gradient and treatment locations alternating biweekly (a total of 10 weeks of sampling, 5 weeks of gradient and 5 weeks of treatment). We use the LiCor 6400 photosynthesis analyzer machine to measure soil temperature and soil respiration, and the HydroSense probe to measure soil moisture. Sampling usually takes only 1-3 days out of the week, so the rest of the week we usually work on our individual tasks, organizing data, running statistical tests, and inputting and analyzing data in GIS. Currently, we have augered samples at each of the gradient locations (organic and mineral layers) and are now processing the soils in the lab for root density, bulk density, and carbon and nitrogen content. We also plan on gathering the leaf area index at each of the gradient plots in the last few weeks to see how biomass affects soil respiration.

While we are still gathering and analyzing our data, we have learned many things about forest ecology and how different variables would affect soil respiration. For instance, we have learned that warm and wet conditions would cause an increase in carbon dioxide efflux, and that microbial (decomposition) activity is higher in the morning and also in the trenched areas (since there is significantly less root respiration).

Tuesday, August 3, 2010

PROJECT PROFILE: Using Computer Science at Harvard Forest to Increase Integrity of Scientific Conclusions

By Sofiya Taskova and Morgan Vigil

This summer, we have had the privilege of working with Dr. Emery Boose and Dr. Barbara Lerner on a project involving a mash up of ecology and technology. For the past few weeks, we have been inundated with the buzzwords "data provenance", "sensor network", "Process Derivation Graphs", "Data Derivation Graphs", "stream discharge", and "weirs". Our headquarters is located in the Shaler Common room (where we do most of our programming and computer work), but we do make a weekly trip out to the six hydrology sites in the forest to collect manual and logged data as well as water samples and measurements for stream ecologist Dr. Henry Wilson of Yale University.

Our work addresses the problem of data provenance--which handles how data is collected and processed, who interacts with the data, what is added to the data, where data originates, when data is collected, and similar questions. More and more, we are using electronic sensors to collect data, which allow for massive data accumulation. However, this huge amount of data comes with a price--sensor drift, sensor failure, logger failure, server failures, and other "technical difficulties". By making data and everything that affects it transparent, data provenance gives integrity to the scientific conclusions drawn from digital data.

Currently, Morgan is working with Little-JIL--a visual programming language that allows informative "metadata" to be captured while raw sensor data is processed into a more usable format. She is focusing on making the process more usable for non-programmers (specifically stream ecologists) by adding a graphical user interface to the process with a setup wizard. She has also revised and built upon the existing Little-JIL process so that more provenance data about input files and .properties files used in the process can be passed on to a DDG.

On a day to day basis, she is programming (mainly working in Java) but also collects water samples and digital data from the hydro sensors in the forest once a week.

So far, she has learned a lot about the software design process, especially with regards to collaborating with scientists from a different field. She has also learned about the importance of creating data management protocol for the sake of reproducibility and reliability.

From here, there are many ways to go with Morgan's side of the project. She would like to see the process abstracted so that a scientist could use it to collect provenance data from any kind of sensor. She would also like to see it be connected to a DDG-creating process. It would also be good to see it developed into an even more usable tool for scientists.

Sofiya is using a graph (a structure that describes relations between the elements - procedures and data instances - that constitute the process) to represent the specific process that a piece of data undergoes. Her goal is to optimally represent the different manipulations of the data and to collect the provenance information of a running process.

The central question that she is addressing is what amount of information to collect about a process. It appears preferable to maximize the details in order to avoid undermining any software functionality that could be of interest. However, massive data sets are very likely to be manipulated in practice, in which case, the amount of provenance information explodes.

On a day-to-day basis, she works on a computer program that collects information on a process strictly defined in the graphical language Little-JIL. She also describes traversals of Process Derivation Graphs (graphs showing all possible execution paths) using Data Derivation Graphs (graphs showing execution paths of particular pieces of data) to help consider the possible handlings of the data and errors that may occur during the process.

While working on the project, she has become familiar with the problem in scientific research of keeping data measurements consistent and adequate for analysis and comparison despite the variation of scientific methods and the myriad of circumstances that may flaw the validity of the data.

In the future, Sofiya is looking to continue working on the software for collecting, storing, and using data provenance information. She is hoping that the basic functionality supported by the software will solve the problem of data provenance in strictly defined processes in many domains including science, engineering, and health care.

Monday, August 2, 2010

STUDENT HIGHLIGHT: The Delicious Food for the Harvard Forest Summer Program

By Sarah Gray

When I arrived at Harvard Forest back in May, I was shy, timid, and scared of my new environment. After meeting some of my fellow REUs, I became more relaxed with my surroundings. After the jitters of my first day subsided (having arrived at the Forest a week after the other students), I realized that I was starving! I asked my housemates if there was any food, and their reply was "Ohh, yes. There is food."

Joe Horn, a fellow REU, led me into the kitchen and told me,"You know the old saying: ‘Never trust skinny cooks?’ Well, here at Harvard Forest, that is not the case." After eating one bite of the cold stir-fry straight from the fridge, I agreed. Since then, I would not only trust Tim and Sarah with my stomach, but my life.

There has never been a meal that was not completely delicious. From the vegetables that are cooked to perfection to the deserts that make you go for fourths, I can't seem to stop eating. When I was younger I always used to joke about the food I wanted served to me when I was on my death bed, and Tim's and Sarah's food makes that cut. One of my favorites were the tacos made with local beef and the perfect spices; the chocolate almond cherry cookies certainly win an honorable mention.

The things I think that have made me gorge and drool were the Strawberry Shortcake Cake and the Triple Chocolate Mousse. My friends here can attest that, on the night of the Triple Chocolate Mousse, I ate about four of them and still wanted more.

Now that the end of the summer program is nearing, I am counting down the final days of eating this delectable food before it is back to Mac & Cheese and PB & J. I will miss Friday morning breakfasts of waffles, blueberry pancakes, and mouthwatering coffee cakes and sticky buns.

So this is a shout out to the cooks, and a huge thanks for keeping our tummies full and happy.