Category Archives: Teaching

I helped develop the curriculum, lab exercises, field trips and instrumental procedures for MIT’s 12.335/12.835 Experimental Atmospheric Chemistry course in its first year (2007). I have TA’d the course four times (2007, 2008, 2010, 2011).

Soil systems – the challenges of complexity and scale

Soils are complex systems, in which physical, geochemical and biological processes interact in aggregate structures situated in dynamically shifting air- and water-filled spaces. It is both difficult to adequately sample soil properties and to model processes related to those soil measurements. These challenges were discussed in a stimulating three-day conference on Complex Soils Systems in Berkeley a few weeks ago. Attendees came from an incredible diversity of backgrounds with a common interest in tackling issues in soil science. An overarching concern was to better understand soils to know “How to feed the soil and the planet?” in the anthropocene, which was a question posed early on by Professor John Crawford. 

Issues of scale were brought up explicitly or were evident implicitly in many of the presentations. Namely, that relevant processes in biogeochemical cycles occur over a wide range of spatial (nano- to mega-meter) and temporal (seconds to millennia), but our observations are typically limited to a much narrower range given measurement and resource constraints. These issues were elegantly summarized in the article “Digging Into the World Beneath Our Feet: Bridging Across Scales in the Age of Global Change” by Hinckley, Wieder, Fierer and Paul in Eos, Transactions American Geophysical Union 95 (11), 96-97. In a real sense, the scale issue presents problems when societal decisions regarding soil sustainability and ecosystem services are made using data and models derived from different (often smaller) spatial scales than the policies themselves.

One illustration of the concept of a spatially complex soil system is illustrated with the figure below by California College of the Arts (CCA) student Sakurako Gibo. The image depicts a theoretical assemblage of soil microbes with different morphologies (for instance round spores versus string-like mycelia). In the second figure, the complex system is “pulled apart” into bins that might represent the effect of a sampling strategy that subsamples the whole system or measurements that only count certain members of the communities. The information about the original complex assemblage and connections is not retained, and as a result, data and rules based off of the binned samples may be different from the case in the real intact community.

Spatially complex microbial community

Spatially complex microbial community

Spatial ordering is lost in measurements and models

Spatial ordering pulled apart

What to do? Well, let’s just say I walked away from the meeting knowing that there are plenty of unanswered questions on soil complexity and scale. With the increasing technical capability in soil and microbial measurements, and communication at meetings like this one, we’ll get there soon.

I’ll end with another neat set of figures produced by CCA student Leslie Greene who illustrated an emergent pattern of predicted H2 consumption (o) based on the availability of H2 (•) from the atmosphere (distributed) and from N2-fixing root nodules (gray filled circles). She created the pattern of H2 consumption based on one rule, soil moisture had to be above 10% and below 50%, as indicated by the concentric rings around water-logged soil sites (red filled circles). From this simple scheme, an irregular pattern emerges of the location where H2 consumption occurs. When faced with the complexity of soil, it is easy to feel paralyzed (for me anyway), and perhaps starting with a simple approach like this will help me embrace the system and its questions.

Emergent H2 system

Emergent patterns of H2 consumption

14

At a slightly more macro scale

Thank you for the BioDesign course organizers at California College of the Arts (Tobi Lyn Schmidt and Mike Bogan)!

BioDesign course – bridging science and art

Biologist/architect team Tobi Lyn Schmidt and Mike Bogan created a course linking artists, designers, architects, and biologist from the California College of the Arts (CCA) and Stanford University. I served as a postdoc mentor to help inspire and guide the process of cross-hybridizing biology and design (some examples) with three really talented undergraduate CCA students: Leslie Greene, Sakurako Gibo, and David Lee.

The students were first charged with creating designs to illustrate scientific concepts in my field of research. I challenged them think about the issue of scale with respect to the biogeochemical cycles I study. The processes I investigate occur over a wide range of spatial and temporal scales, which is a challenge for their measurement and interpretation. David focused on a selection of atmospheric trace gases with a wide range of abundances, and that interact with each other through key reactions. In his image, the hydroxyl radical (OH) is illustrated by the white dot from which orange and blue strings respectively represent the path length to molecules of  hydrogen (H2) and methane (CH4) in the surrounding space. The density of the strings is representative of the concentration of H2 and CH4 relative to OH. I love the sense of competition in this image. These reduced molecules compete for reaction with OH, and with other trace gases not shown, which helps explain the relatively their long lifetimes of H2 (~2 years) and CH4 (~10 years) in the atmosphere.

Concentration Burst, by David Lee

Concentration Burst, by David Lee

The second task for the students was to manipulate a biological system for design or artistic ends. All three students visited the Welander geobiology lab at Stanford and the Berry lab at Carnegie on campus where atmospheric trace gases are measured. For her project, Leslie was interested in manipulating microorganisms to reveal art. Using a combination of strains from the lab and purchased online, Leslie created competitive interactions between organisms and against antibiotics to reveal structures that were both patterned and complex. In the example below, she laid a cross-pattern of Streptomyces ghanaensis and Bacillus subtilis colonies and let them grow and compete. Intriguing features arose, appearing as if the Streptomyces strain grew on top of the Bacillus strain, perhaps antagonistically or not. Leslie overlaid emergent patterns in topology and color from microbial cultures with and without competition to create an amazing image that reveals some very aesthetic order in the systems.

Bio-manipulation of Streptomyces ghanaensis and Bacillus subtilis

Bio-manipulation of Streptomyces ghanaensis and Bacillus subtilis

Emergent patterns from competition

Emergent patterns with and without competition

 

Finally, the students illustrated various concepts related to my work including artistic renditions of Streptomyces colonies and concepts of complexity (see related post). I really love the feel of the image created by Sakurako Gibo showing the atmospheric H2 concentrations that I measured between the ground and top of a measurement tower (y-axis) over the year-long experiment (x-axis) at Harvard Forest as an ephemeral curtain. Higher concentrations of H2 are represented with a deeper intensity of blue. The impact of the soil sink is illustrated by the lightening of the color near the base of the image caused by high rates of soil microbial H2 consumption in summer and fall.

Curtain of H2 Harvard Forest

Curtain of H2 at Harvard Forest, by Sakurako Gibo

 

Field trip around Boston for the MIT Experimental Atmospheric Chemistry course

It’s my fourth year as a TA for our ‘Experimental Atmospheric Chemistry’ undergraduate and graduate course at MIT, and today we have loaded up the department’s van with nitric oxide (NO) and ozone (O3) monitors, a uv radiometer, and three particulate monitors (PM 10, 2.5, and 1.0 um). As part of the ‘Pollution Exposure’ unit, we will synchronize the monitors and drive around Boston noting changes in pollutant levels and keeping notes to identify possible pollutant sources. The field trip is a good time, and this year our class has grown to ten students, which is the biggest class we’ve had since I helped develop the course in 2007 with my advisor Professor Ron Prinn and group alumnus Arnico Panday, now at University of Virginia.

We explore tunnels (Boston’s Big Dig provides miles of them), construction sites, urban sites with high traffic congestion, and cleaner beach sites. The students note changes in particulate levels at different sites, which often have distinct particulate size distributions as you would expect from a variety of types of aerosol sources. We follow cars, trucks, and buses of all shapes and sizes. Diesel buses and accelerating vehicles have much higher particulate emissions than clean natural gas buses and stationary vehicles; we might already expect this, but students are able to witness it first-hand and real-time.

Tunnels provide a unique photochemical ‘experiment’. Outside air, under uv light from the sun, has certain levels of pollutants that are created and destroyed by ‘photochemical’ reactions. When this air is swept into a one-way tunnel by the traffic and moved slowly through the tunnel, the tunnel blocks the sun and air is no longer being acted on by uv light, so the photochemical reactions cease. Students can then watch what happens if certain reactions that don’t need uv light proceed (such as NO+O3-> NO2 + O2, which will decrease concentrations of O3) and certain reactions that need uv light are halted (such as NO2 + uv -> NO + O leading to O + O2 + M -> O3 + M, which would have regenerated concentrations of O3). In the tunnels, ozone concentrations decrease because O3 reacts with NO, and because there is no uv light, ozone cannot be regenerated; the students clearly see ozone concentrations fall to nearly zero by the end of long tunnels, such as the Ted Williams Tunnnel in Boston.

The study of atmospheric chemistry is often the study of invisible reactions producing invisible products in the atmosphere, so driving around with instruments and observing these phenomenon real-time have been invaluable teaching tools for students (and myself). Over the semester, the course includes the following sections and field exercises; 1) CO2 and climate, in which students deploy a CO2 monitor to Harvard Forest to understand the carbon cycle, 2) Pollution exposure, in which students monitor their own daily particulate exposure and also observe pollution around Boston as described here, 3) Photochemical cycles, in which a wide range of instruments are deployed to MIT’s Green Building roof, which is the tallest building in Cambridge, and the concentrations of chemicals linked by photochemical reactions are studied in detail, and 4) Isotopes and the carbon cycle, in which students learn the value of the added information provided by measuring the isotopic composition of atmospheric molecules, not just concentrations, and measure the isotopic composition of some atmospheric trace gases. Isotope expert, professor Shuhei Ono, has joined the course and spearheads this fourth topic on isotopes. I have enjoyed helping develop and teach this course, and along with the students I learn something new every year!

DEAPS Extreme Weather and Climate 2011

This week I traveled up to Mt. Washington with this year’s EAPS FPOP (Freshman Pre-Orientation Program) Discover Earth, Atmosphere and Planetary Sciences: Extreme Weather & Climate. It’s the third time I’ve acted as a TA for the program by heading up the flora and fauna section, or what is now more commonly known as “Flora with Laura.”

Describing the link between vegetation and microclimate in the Alpine Garden

The 3 day program is Spotlighted on the PAOC website, which describes it as being “designed to provide incoming freshmen with the opportunity to explore the science of weather and climate through an exciting combination of lectures and fluids experiments, providing a glimpse into some of the most interesting and challenging aspects of research in PAOC.

I’ve always be interested in plants. My father (and now one of my sisters) is a forester in the diverse mixed forests of Southern Oregon. The flora of trails I’ve hiked always interested me, especially the relationships between plant communities and regional climate (and even micro-climates) that were obvious even to my untrained eyes. Shrubby grasslands cover convex faces of the hills in Big Sur, CA, while coastal redwoods thrive in the moist and cool concave recesses. The towering forests of the North Cascades, WA are a world apart from the flowering cacti of the Mojave. However, it wasn’t until I took the Field Course in Arctic Science, held at both the University of Alaska, Fairbanks and the remote Toolik Field Station on the North Slopes of Alaska, that I formally learned about the adaptations of plants (and animals) to climate. We focused on different strategies plants employ for survival in harsh environments, specifically to arctic environments.

The material from that course translates beautifully to Mt. Washington because, just as plants adapt to the harsher climates found at higher latitudes, the plants found at different altitudes on Mt. Washington must adapt to increasingly harsher alpine conditions. Therefore, the altitude gradient on a mountain in Massachusetts reflects the latitudinal gradient from Massachusetts to the northernmost reaches of Alaska. Interestingly, many of the species on the summits of New England are also found in northern most Alaska – the alpine mountain top climes are the last refuge of arctic plants that extended to mid-latitudes during the last ice age.

The DEAPS group ascends the Mt. Washington auto road from the base near Pinkham Notch at 2032 ft to the peak at 6288 ft. The students make temperature, wind speed and pressure measurements to note how the weather varies up the mountain on that day. I teach them how to use the plant ecosystems as the key indicator of the year-long weather experienced at different altitudes on the mountain. The presence of plants that are adapted to cold temperatures, short growing seasons, ice and wind abrasion, high uv light, low water and nutrient retention, and other environmental stresses are visual indicators of the harshness of the year-round weather on Mt. Washington. Students note how these hardy plants increase in prevalence as we ascend the mountain, which confirms their lessons in how weather up the mountain also becomes more extreme.

DEAPS group at the Mt. Washington summit

Beyond the actual instruction, it’s a unique opportunity to interact with incoming MIT freshman; often we are the first group of MIT students and staff that they interact with upon arrival. Students come from all over the country and the world, and they are eager to start their academic and personal lives at MIT.